-It is not certain that the Final Cylon is behind everything; if it is Boomer, she probably doesn't even realise she is the Final Cylon, just like she used to think she was human. The "Head People" may be a better candidate for being "behind everything". That she was in opposition to the final four at times is thus not really a problem - on New Caprica, the four weren't even aware they were Cylons.
-Since Boomer can download in what appears to be, and probably is, the body of an 8, it seems clear that she is at least compatible with the 8s (if downloading is no problem, why would memory sharing be?). How this is possible (her being not an 8 - sort of, yet seemingly identical), is the weak point of this theory. However, don't count out that RDM can find some explanation for this. For example, the 8s could be a copy, perhaps with some subtle changes in their base programming/personality, of Boomer's model, only made many years later.
-Caprica-6 was actually not a sleeper agent; she was fully aware of being a Cylon, whereas Boomer had no doubt (until "Water", at least) that she was fully human. She is the only "sleeper", of the 7 known models, that we've heard about. The Dylan Four are the only others who did not realise what they were.
The idea for Boomer is based on those points, most of which you mentioned in some form in your post:
1.RDM saying repeatedly that no person in the last supper picture is the fifth
2.D'Anna saying there are four Cylons in the fleet, while also threatening to kill a number of colonials on the baseship (between those first 2 points, a lot of candidates seem to be eliminated)
3.Boomer would be back "big time" in S4, according to writer Taylor (hasn't happened in S4.0, so I suppose it's yet to come in S4.5)
4.Boomer is in major need of redemption and can be said to still be in the shadow (fits the Razor prophecy quite well)
5.we have been promised that the reveal of the final Cylon will mean something; it will be "organic" and "satisfying" from a dramatic POV, not "a day player from season 1". Boomer is a fairly important character, in the show from the very beginning, has a complex relationship to a number of other characters (Adama, Tyrol, Tigh, Anders, Starbuck, Gaeta, Caprica-6, D'Anna, Athena) which could be exploited from a dramatic POV. Boomer is a very conflicted character with love/hate relationships to both colonials and Cylons, as she is a Cylon who deep-down feels more human than Cylon, yet has been rejected by the humans because of the whole sleeper agent thing (where she presumably had no influence over). Interestingly, she is also the one who put the lion's share of the rag-tag-fleet together, back in the mini.
6.We have also been told that almost no guess has been correct (a number of weeks ago). Since she is a known Cylon, very few people would expect her to be it.
7.there are arguably a few audiovisual hints that point to Boomer (allthough I'm aware those exists for many other characters as well, and each could be a red herring or coincidence or misinterpretation by me):
a. the music that plays in "Revelations" when D'Anna recognizes the final four on Galactica's hangar deck, is very close to what is played when D'Anna turns her attention on Boomer for the first time on "The Hub". Could be a new theme for D'Anna personally, but IMO it is quite telling and connected to the ID of each of the five.
b. When Tigh confesses to Adama that he is a Cylon in "Revelations", he literally says "like Boomer... [pause]...I'm one of the final five". Disclaimer: I'm cheating by putting two sentences together so the result is out of context (he's saying that he was unaware of being a Cylon, like Boomer, and thus he is one of the final five - Tigh obviosuly doesn't know who the 5th is). But I thought it was pretty remarkable that this line was written in this way, like the writers were giving a wink to the audience
c. Early in S4.0, one of the 8ths wondered if the final five looked anything like "us" (that is, the Cylons of the 7). Since I think it is a given that the final five are human looking just like the other numbered Cylon models (so, not Kara's Viper or Jake the dog), she seems to be effectively wondering if their outward appearance might be similar to one of the 7 known models. Well, she just could be on to something here, as Boomer looks like her twinsister.
d. D'Anna has a personal reaction to one of the FF when she recognizes it; surprise ("you?") and an apology ("I had no idea...") follow. It seems like someone she knows, wasn't very kind to and didn't expect. Anders is a perfect fit (because she very personally tried to kill him), but so is Boomer. Had the writers already decided who the Dylan four were, by this point? From what I've heard the final decision wasn't taken until "Crossroads" was filmed. In that case, the apology is quite likely aimed at the one Cylon that the writers had already firmly in mind as being the final one.
People like Roslin or Adama or Baltar, which were on the baseship when D'Anna said there were four in the fleet, are tempting as final Cylon, but the problem is that they are in the last supper picture and RDM has again confirmed that those are not the final Cylon. So, to find other candidates then Boomer you have to either consider dead (or believed dead) characters of reasonable importance (say, Ellen Tigh or Helena Cain), or find some way to explain why D'Anna could be wrong/lying about the 5th not being in the fleet. The latter requires a theory not any less convoluted than the Boomer one, though.
Or you can maintain that RDM is outright lying and continues to do so, but I think that's very unlikely.