I can't speak of this one source you're quoting, but I myself have witnessed censorship on this topic. I've seen kippot photoshopped onto prior Rabbanim. I've quoted the article on kippot censorship topics on this answer elsewhere on Mi Yodeya. I've also had experiences of Rabbis trying to force me to censor my family's minhag regarding Kippot. Since you are an Egyptian Jew I'm sure it would not shock you that most Egyptian Jews did not wear a Kippah outside of the synagogue in Egypt. I have family pictures of Bar Mitzvot in which some people in the pictures aren't even wearing Kippot. And yet current Rabbis have no issue telling you to practice your minhag, but also tell you if you don't wear a kippah you are breaking the law and they expect you to censor your family minhag for the sake of current practice. Another topic that I see similar censorship practices concern women, prayer, tefillin, and tallits.
Rabbi Messas discusses women praying or holding study sessions wearing tefillin in Sephardic lands, it was not a controversial statement at the time because he was just reporting on what he had read from books discussing the topic. Fast forward to 2015 and when his book is republished, that section is removed in its entirety.
R. Joseph Messas has a passage, now famous among the Orthodox
feminists, in which he refers to an unnamed book that mentions that in
Spain there were places with women’s prayer groups at which each woman
wore a tallit and some wore tefillin. It appears in his Nahalat Avot
(Haifa, 1980), vol. 5:2, p. 268.
In 2015 the multi-volume set of Nahalat Avot was reprinted in
Jerusalem. Take a look at the following page and you will see that the
passage dealing with the women’s prayer groups has been deleted in its
entirety.
....
Unlike Ashkenazic internal censorship of this sort, Sephardic
censorship is a relatively new phenomenon (only a few decades old).
Here is another example. R. Isaac Abraham Solomon’s book Akim et
Yitzhak was published in Baghdad in 1910. On pages 112b-113a he
rejects a position of the recently deceased R. Joseph Hayyim, the Ben
Ish Hai.
R. Solomon appears to even cast doubt on R. Joseph Hayyim’s integrity
when he writes:
וקי”ל ת”ח שאמר מילתא לאחר מעשה אין שומעים לו להחזיק דבריו
This book was reprinted in 1971, and here is how the pages look.
Source with pictures: https://seforimblog.com/2015/11/maimonides-and-prophecy-r-pinhas-lintop/
I'm not aware of this kind of mentality existing in diasporic Jews of the Middle East until relatively recently. The Cairo Genizah famously holds many fragments of things that are outright heretical today. Ketubot in which women could initiate divorce, Angelic letters, Hebrew copies of Ben Sirach and other documents. These documents show a tendency to preserve minority opinions, even after they aren't usable anymore. Whereas in our times a lot of orthodox institutions would throw such things in the trash.
For example, I remember when a local Chabad house I attend attempted to throw away my personal copy of the Soncino Chumash. I had stored it there for services because I found the other Chumashim from Chabad contained so much interpretation in their translation that I felt like I could never understand the text in the Peshat. Another congregant stopped the Rabbi and called me. When I went to pick it up I saw they were culling all books that did not contain "strictly orthodox commentary." This is also a form of censorship.
Update: Another answer here mentions censorship of certain halakhic opinions as almost like a safeguard for uneducated Jews. I think a good example of this, and something I've personally gotten push back for is the laws of baking matzah. If you open up the Mishneh Torah and the Shulchan Arukh it's clear and obvious the rule is you have ~18 minutes from the moment you stop kneading dough to bake it or else it's chameitz and should be burned. And yet most publications in our time obscure these opinions and state the halakha is that the entire process must be done within 18 minutes by Jews only. Imagine my surprise to read in Minhagei Misrayim that they would hire local non Jewish bakers to bake matzah for Pesah.