There were also things like mobility and, for me at least, the fact that a tower would be unwieldy since we would have to fit a dragon in it and have easy ways in and out. An altar, on the other hand is probably shaped to avoid that. Though I do have to admit a Tower would probably allow for more regular usage, which would be interesting.
Also, just thinking, but without an active time-limit on when the dragon turns back—assuming that's still true—wouldn't it theoretically be possible to just stack uses, so long as the time between isn't too long? Like, sure, if it takes a week or a month between uses, that'd be bad, but what if it only takes a day to recharge? If we just waited a day or two, we could theoretically gather two or three dragons to use at once. Of course, this only works for offenses, since defenses are rarely that lenient with time, but it's a thought.