Hi
Yes there are many scenarios and I understand this. It is about making options available that suit different ones.
In our case if I have Vendor A is in USD and Vendor B in CAD and myself say is Vendor Alpha (base shop and currency) GBP. Vendor A has a shop page in USD and when I pay him, he wants his commission in USD. Vendor B likewise etc. This is also my preference as I set products (versions of) per geolocation as they are priced differently.
Different multi shop set ups will require different options, but I don’t think there are too many variations that would satisfy all.
So when you mean shop base currency I would prefer to say Vendor Shop Base currency rather than site base currency.
Commission in order currency I think is not a good approach, so I agree.
There is a good discussion here on a rival product forum, but issues are the same of course.
With you Booster product combined with Marketplace, I am sure that you could cover most scenarios. That really would be a JetPack
https://www.wcvendors.com/help/topic/currency-switcher/
I hope this helps.
Haider