Those are warnings and not errors. Distributing plugins for different edition of a game and/or for different versions of a game in a single distribution is valid. This apply to all xSE extenders.
I'm curious, what purpose would this serve in the case of a game that hasn't been updated in many years and likely won't see an official update again? (New Vegas) I suppose a FOMOD installer could be used if there are a handful of versions floating around?
These same warnings can lead to CTDs (particularly in the case of Skyrim/Skyrim SE). You can dismiss the warnings using the little cog next to the warning notification if you believe they are irrelevant, although I think that currently ignores them for all games.