You're okay. I think "control point" victories are fine, as long as they're a game setup option (and not on by default). "Shrines" could still have a gameplay effect (in DE they could trickle glory, for example), even if the control point victory is not enabled by the host.
I think biomes could have different "shrine" models. Sahara and Nubia biome shrines could be based on the current Ptolemaic temple actor. Those actors are based on sacred complex "kiosks" anyway, not actual temples. In an Italian map, the shrine would be based on the Temple of Vesta. In a Greek map, I think the shrine would look like the Temple of Athena Nike or the "Athenian Treasury" at Delphi.