As you observed, FT3 is focused on world-scale to regional things, which is why use of map projections is an important part of its user experience. It has a constant-size editing setup, which means that you can't just add detail where you need it, but have to have the same editing resolution everywhere, even in the middle of the ocean. To get better editing resolution in FT3, you need to use Map>>World Settings:Editing page and set the resolution to something higher. The default world editing resolution is 256x128, which is about 157 miles per sample on an Earth-sized world. The resolution will go up to 8190x4095, which is about 5 miles per sample on an Earth-sized world.

FT3 has a horrible climate model because it doesn't take into account heat movement via wind or ocean. It does take into account a number of useful things, and the rainfall/temperature models do take into account the underlying terrain, so it has some useful features. It definitely won't generate the kind of detailed microclimate things that you seem to be looking for.

Wilbur works reasonably well for smaller areas (100 mi on a side is about its sweet spot for normal editing). Wilbur is not particularly plausible for whole-world areas, but it's usually good enough for visualization purposes. Wilbur doesn't have anything resembling a climate model at all, so it can't help you there.

As far as software that would work for the microclimates present on a 70x70 mile area, I don't think that I've seen any. Temperature and rainfall models require global (or at least fairly large-area) effects for things to be particularly meaningful. If you want local-area things, then you need to provide information that would be derived from such a global model such as wind patterns and rainfall schedules.