Won't make any difference - the descr_strat doesn't check if a building is "allowed" before placing it. The only difficulty comes if it's destroyed or downgraded by settlement sack - in which case you couldn't rebuild it.
We do also take note of major cults that are attested to in particular settlements, when deciding which temple, but it's all still educated guesswork.
The only script-linkage I can think if is for the Sabaens, I'm sure they require a particular type of temple in their capital for a reform event.
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