First off, I really like that makemkvcon now tries to construct an filename using disc titles. A small improvement would be to construct the filenames with track number last like this:
Title_Of_TV_Series_Season_3_Disc_1_t02.mkv
rather than the current method which does this:
t02_Title_Of_TV_Series_Season_3_Disc_1.mkv
Why make the change? So that the when the filenames are alpha sorted, they're are in the right order. Dealing with groups of them by disc or season becomes trivial.