Once again. Mods like HotA and WoG work by patching original H3 SoD executable and this is reason why they’re not compatible with each other.
VCMI engine have nothing to do with original H3 executable, but it’s support same formats and feature set (and some of WoG features). There is built-in mod support in VCMI, but no support for alteration of map sizes because UI is not moddable. Though both our RMG (random map generator) and engine can support maps of any size and form-factor, but somebody still have to implement UI that going to expose it to player.
Also you can already install as many towns as you want and VCMI will handle them all just fine. If you use latest development build then random map generator will also use map objects, heroes and creatures from mods you installed.
As @Warmonger said there no such thing as “wog options” in VCMI. The reason is because VCMI adoption of that mod don’t use anything from original WoG except art assets. This is as well true for HotA adoption.
WoG features that are supported by the engine are always enabled when mod is active. Some of features like stack experience can be also enabled without WoG.