However there is a long ongoing discussion that the two episodes actually belong to season 04, but TheMovieDB will not change that.
My question is, can I configure Infuse to get meta data for the first episodes of season 4 from TheMovieDB and have my own local meta data for the last two episodes, so Infuse can show season 4 “correctly”?
You can name these like @munpip214 said, and Infuse would group them with the other season 4 items. If those episodes aren’t listed on TMDB then you would just get general series info (artwork and descriptions) instead of episode specific info.
Adding your own NFOs and artwork for those 2 episodes would give you episode specific info.
This will work for displaying in Infuse, but you won’t be able to sync watched history for those items to Trakt, since they rely on TMDB’s order.