The reason for two days of yontif (outside Israel) is based on uncertainty about the date due to distance from Jerusalem and time needed to travel to convey the news of when the month started. The reason we have two-day Rosh Hodesh is explained here.
What puzzles me is why we do not have two days of Rosh Hodesh for the same reason as we have two days of yontif. Why doesn't the reasoning for two-day yontifs apply to Rosh Hodesh (yielding a two-day Rosh Hodesh every month)?
I am excerpting parts of Ramba"m, Hilchot Kiddush Hachodesh, as I believe are relevant to your question. In summary, the 2 day Yom Tov was based on the distance that messangers could travel within the first 10 days of the month (based on # of allowable travel days for Tishrei. It seems that calculation of the 1st day of Succot was most important. Rosh Hashanna had already been established as 2 days even in Israel, according to most opinions. Yom Kippur, I think, was made 1 day even in Galut b/c of the danger of fasting 2 days - have to check this further.) as well as the establishment of Jews in that village during time of Sanhedrin. Now, the two day celebration is based on following the previous custom and according to Ramab"m is takanat sofrim.
As you already saw, the doubt of Rosh Hodesh is different, as even those in Israel weren't sure, so potentially, every month could have days Rosh Hodesh. It didn't happen that way, but I believe there were times when you had 2 consecutive months with 2 days Rosh Hodesh, depending on when witnesses appeared. While Ramba"m doesn't outrightly state this, I infer that those in the far distances who had the doubt of having to observe 2 days Yom Tov, also observed 2 days Rosh Hodesh every month. (Would appreciate if someone could confirm or refute this.
Mishneh Torah, Sanctification of the New Month 3:11-12:
Every place that the messengers reach, they'd make the festivals a one day holiday as is written in the Torah. And the distant places that the messengers wouldn't reach would make two days because of the doubt, for they wouldn't know which day was the day that the court fixed the first of the month. There are places that the messengers of Nissan would reach them and the messengers of Tishri would not reach them. And according to the law, they ought to make Passover one day of holiday, for the messengers reached them and they knew on which day the first of the month was fixed. And they ought to make the holiday of the festival of Tabernacles two days, for the messengers didn't reach them. And in order not to distinguish between the festivals, the sages amended that any place that the messengers of Tishri didn't reach would make two days [of holidays], even the holiday of Ceasing (Shavuot).
Mishneh Torah, Sanctification of the New Month 3:13:
And how much is between the messengers of Tishri and the messengers of Nissan? Two days. For the messengers of Tishri didn't travel on the 1st of Tishri because it is a holiday and not on the 10th of it because it is the Day of Atonement.
Mishneh Torah, Sanctification of the New Month 5:12:
A place that has between it and between Jerusalem 10 days or less than 10, and it is [in] Syria or the outside of the land [of Israel], and they don't have a custom. Or it is a newly formed city in the desert of the land of Israel. Or a place that [people of] Israel dwells now. They make two days like the custom of the majority of the world. And every second day holiday is from the words of the scribes and even the second day of the holiday of Rosh Hashanah which everyone makes at this time.
Rmaba"m's discussion is mainly in chapters 4 and 5, and, to get a better perspective, you should read the majority of these chapters. The English translation was copied from sefaria.org.
In summary, we aim to get 1 day for both. Rosh Hodesh has its "internal" problem both because of the moons orbit which is not a full day, and when witnesses appear. However, once we know when Rosh Hodesh really was, we can't correct time that already passed (i.e. we can't "correct" Rosh Hodesh itself If people already observed the 1st day, and it was a 30 day but it really was 29.) However, once we know which day really was Rosh Hodesh, we attempt to inform people of that, afterwards. But, there is only so much time and distance that messengers can travel, so they are ALWAYS doubtful.
There is a separate discussion in Ramba"m in ch. 5, I believe that discusses if the date of Rosh Hodesh can be "reverted" retroactively. See there. It's somewhat tangential to answering this question, and I didn't want to cite from it, here.
every rosh hashana was 2 days for almost everybody for reason see Rambam kidush hachodesh 5 law 7-8 (in short: even if the witnesses came on the first (30th) day the court did not send messengers until after the first day was over (only jesuralem knew about it))
from there it seems that since rosh chodesh was not yomtov so they sent the messengers on the day of rosh chodesh (so more of israel knew about it (that rosh chodesh was only on the 30th day) not only jerusalem)
so the question is not why not have all rosh chodesh 2 days, but why now that we use a set calendar do we have 2 days rosh hodesh
Rambam - Kiddush HaChodesh - Chapter Eight - Halacha 4
According to this reckoning, the thirtieth day of the month is always established as Rosh Chodesh. If the month is lacking, the thirtieth day will be Rosh Chodesh of the coming month.
If the month is full [the coming month will have two days that are Rosh Chodesh]. The thirtieth day will be Rosh Chodesh, since a portion of it is [fit to be] Rosh Chodesh. [Nevertheless,] it will be counted as the completion of the previous month, which was full. The thirty-first day also will be Rosh Chodesh, and the reckoning [of the days of the coming month] will start from it. It is the day established [as Rosh Chodesh].
Thus, according to this calculation, there are some months that have only one day Rosh Chodesh, and other months that have two days Rosh Chodesh
שהם וישפה on this rambam asks this question and does not like the answers he found
From this answer from your link you can look on it as on the 30th day we make is rosh chodesh just in case the witnesses come on that day, in a 29 day month we look at it as the witnesses came (before the end of the 30th day), but in a 30 day month we look at it as if the witnesses did not come yet so now we hold the 31st day as rosh chodesh (and we look at it as though the witnesses came this (the 31st) day and it becomes the first day of the month)
The Takkanah to keep two days of Yom Tov is to continue what used to be done outside of Eretz Yisroel. They kept two days since they weren't sure which day is Yom Tov, and doing work on Yom Tov would be violating the Yom Tov. This only applies to Yom Tov.
Besides, there was never a two days Rosh Chodesh in Bavel. They weren't sure which day is the right one, but there is no real observance of Rosh Chodesh. Rosh Chodesh is mainly about the Beis Hamikdash.
Moreover, if we were to always keep two days of Rosh Chodesh that would mess up our schedule and we would be very confused about which day we are counting from. This would ruin the calendar.
