I think that it would likely be incorrect to ever use the source constraints with a tool. An example: if you have a formatter or linter that checks for a Python 3 specific condition and you run it on code whose transitive constraints are actually only valid for Python 2, you will break that code.

Hm. Actually, I think that this applies regardless of source/transitive... the tool would need to be aware that the code was trying to be compatible with both interpreters, regardless.