This is a very interesting comment. I did not find anyone who asks your question explicitly, but I found some interesting sources and I have a Chidush that I think may answer it.

1. The Tiklin Chadetin in Shekalim (5a, DH Rebbi Meir Omer) writes that the reason why Rebbi Meir maintains that the Kalbon money must be given for Shekalim is that he is consistent with his opinion (on 4b) that "in the same way that the Shekel is stated in the Torah, the Kalbon is stated in the Torah." This statement shows that according to Rebbi Meir the Kalbon has the same status as Shekalim themselves.

2. The Rambam (Hilchos Shekalim 3:7) makes it clear that the Halachah does not follow the view of Rebbi Meir. He writes that "the Kalbonos are not Shekalim, but rather the 'Shulchanim' (who collect the Shekalim throughout the country) leave them aside separately until Hekdesh is able to use them."

The Ra'avad writes very briefly that there are many disputes about this in the Tosefta and the Yerushalmi. The Ra'avad does not explain what he means by writing this. The Kesef Mishneh explains that Rebbi Meir is a lone opinion among the other Tana'im who all maintain that the Kalbon is not like Shekalim, and this is why the Rambam does not rule like Rebbi Meir. The Kesef Mishneh adds that since the Rambam was in doubt about whom the Halachah follows among the Tana'im, he therefore wrote in a non-committal way that the Kalbonos are left aside on their own.

3. I saw that the Frankel edition of the Rambam cites the Aruch ha'Shulchan who writes that the Kesef Mishneh's assertion that the Rambam was in doubt about whom the Halachah follows is improbable. The Frankel edition also cites the Rashash in Menachos (108a) who asks that since the Gemara there records the opinion of Rebbi Meir, why did the Rambam not rule this way?

4. Perhaps we may suggest a big Chidush to answer all of these questions. The point is that the main thing the Rambam wanted to teach is that the Halachah does not follow Rebbi Meir. Rebbi Meir's Shitah is that the Kalbon is exactly the same as the Shekalim. The other Tana'im disagree with this and say that the Kalbon does not possess the Kedushah of the Shekalim. It may even be that there is no dispute l'Halachah among the other Tana'im. It is possible that each one simply gives an example of different things for which the Kalbon may be used; they did not intend that it must be used specifically for this thing. All the possibilities that the Tana'im mention are connected with Kedushah of Korbanos; for example, it is used for the wages of the Shulchanim or for the transportation expenses involved in bringing the Shekalim to Yerushalayim. These usages are all for the benefit of the Korbanos, because they enable the Shekalim to reach Yerushalayim quickly so that they can be used to buy Korbanos.

5. We now understand why the Rambam writes that the Kalbonos are left aside separately until the Beis ha'Mikdash can use them. The main thing is that they will be used for the purpose of Hekdesh; it does not matter exactly how. According to this, one does not have to say like the Kesef Mishneh that the Rambam was not sure about whom the Halachah follows because the Rambam maintains that the Halachah does not follow Rebbi Meir. Rather, there is no actual Halachic dispute between the other Tana'im; each one gave a different possibility for the usage of the Kalbonos.

The question of the Rashash is also answered, because Rebbi Meir is a lone opinion, as the Kesef Mishneh writes, and even though only one other opinion was mentioned in Menachos 108a, the Yerushalmi that you mentioned records several Tana'im who disagree with Rebbi Meir.

6. And we now understand why there are so many diverse reasons -- and such an extreme range given -- for where the Kalbon money goes, because they are all valid possibilities, and the crucial thing is that the source to which it goes merely must possess a connection with the Beis ha'Mikdash and the Korbanos.

Kol Tuv,

Dovid Bloom