I suppose it is technically possible to find some sort of compatibility issue. In practice, I have not found or heard of any. I have used Experience Builder 1.11 and 1.12 with Enterprise 10.9.1 without encountering any compatibility problems.
Experience Builder is mostly just a skin over the 4.X Javascript API, so it really never needs to interact with an Enterprise portal for more than very basic functions like loading data.
GIS Developer
City of Arlington, Texas