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Well, I wouldn't say that Tower is in a bad spot on MM6 and similar templates. After all, Griffin Conservatories and Hives are taken just fine by Tower as well, and they are distributed regardless of faction.
Tower is simply, on average, one or two days behind in tempo due to the difficulty of buying and the need for upgrades, hence the troubles. But the variance in map layouts is much higher.
Plus, there is a trading mechanic that partially corrects Tower's finances.
In Schism's Race II, if you remember, 2 out of the 3 registered Towers made it to the semi-finals.