The Rambam's ruling is based on the Mishna in Rosh HaShana (26b):
שוה היובל לר"ה לתקיעה ולברכות
Yom Kippur of the Jubilee Year is the same as Rosh HaShana with regard to both the shofar blasts that are sounded and the additional blessings that are recited in the Amida prayer.
The simple answer to your question is that the Anshei Knesseth HaGedolah enacted the tefilloth when the Second Temple still stood and when the Yovel was kept Rabbinically and to keep track of the Shemittoth (see Ramban [cited here] on Gittin 36a; see also Rabbeinu Tam, cited by Tosafoth d"h "bizman", who held that Yovel was biblical law then too.)
See also Arakhin 32b:
מקיש ביאתם בימי עזרא לביאתם בימי יהושע מה ביאתם בימי יהושע מנו שמיטין ויובלות וקדשו ערי חומה אף ביאתן בימי עזרא מנו שמיטין ויובלות וקדשו ערי חומה... ומי מנו שמיטין ויובלות השתא משגלו שבט ראובן ושבט גד וחצי שבט מנשה בטלו יובלות עזרא דכתיב ביה: (עזרא ב, סד) כל הקהל כאחד ארבע רבוא אלפים שלוש מאות ששים הוה מני דתניא: משגלו שבט ראובן ושבט גד וחצי שבט המנשה בטלו יובלות שנאמר: (ויקרא כה, י) "וקראתם דרור בארץ לכל יושביה" - בזמן שכל יושביה עליה ולא בזמן שגלו מקצתן. יכול היו עליה והן מעורבין - שבט בנימין ביהודה ושבט יהודה בבנימין, יהא יובל נוהג - תלמוד לומר: "לכל יושביה" בזמן שיושביה כתיקונן ולא בזמן שהן מעורבין. א"ר נחמן בר יצחק: מנו יובלות לקדש שמיטין
...he compares their arrival in the days of Ezra to their arrival in the days of Joshua: just as at their arrival in the days of Joshua they counted the years of release and the Jubilees, and consecrated cities encompassed by walls, thus also at their arrival in the days of Ezra they counted the years of release and the Jubilees. and consecrated walled cities... But did they count the years of release and Jubilees [after the return from Babylon]? If even after the tribe of Reuben, the tribe of Gad and the half-tribe of Manasseh went into exile, the Jubilees were abolished, should Ezra in connection with whom it is said: The whole congregation together was forty and two thousand three hundred and three score, have counted them? For it was taught: When the tribe of Reuben, the tribe of Gad and the half-tribe of Manasseh went into exile, the Jubilees were abolished as it is said: And ye shall proclaim liberty throughout the land unto all the inhabitants thereof, i.e., [only] at the time when all the inhabitants thereof dwell upon it, but not at the time when some of them are exiled. One might have assumed that if they were there, but intermingled, the tribe of Benjamin with that of Judah and the tribe of Judah with that of Benjamin, that even the [laws of the] Jubilee should apply, therefore it is said: ‘unto all the inhabitants thereof’, which means, only at the time when its inhabitants are there as [where] they ought to be, but not when they are intermingled! — Said R. Nahman b. Isaac: They counted the Jubilees to keep the years of release holy.
Even if we had wanted, for some reason, to say it was enacted only for the future, we could still suggest that the enactment reflected the general idea of "mehera yibaneh hamikdash" which, at a practical level, reflects that when Moshiach comes, it might be useful to have laws already prepared, and, at a deeper level, reflects the daily aspirations and hopes of the exiled nation.
See also, e.g., Rosh haShana 30a:
ושיהא יום הנף כולו אסור: מ"ט מהרה יבנה בית המקדש ויאמרו אשתקד מי לא אכלנו בהאיר מזרח עכשיו נמי ניכול
ולא ידעי דאשתקד לא הוה עומר האיר מזרח התיר השתא דאיכא עומר עומר מתיר
The mishna taught: Rabban Yoḥanan ben Zakkai also instituted that for the entire day of waving the omer offering, eating the grain of the new crop is prohibited. The Gemara asks: What is the reason for this ordinance? The reasoning is that soon the Temple will be rebuilt and people will say: Last year, when the Temple was in ruins, didn’t we eat from the new crop as soon as the eastern horizon was illuminated on the morning of the sixteenth of Nisan, as the new crop was permitted immediately? Now too, let us eat the new grain at that time.
And they do not know that last year, when there was no omer, the eastern horizon illuminating, i.e., the morning of the sixteenth of Nisan, served to permit the consumption of the new grain immediately. However, now that the Temple has been rebuilt and there is an omer offering, it is the omer that permits the consumption of the new grain. When the Temple is standing, the new grain is not permitted until the omer offering has been sacrificed.
