Using include/exclude lists is a solution (and I will use it for the short term), but not an ideal one. While creating my static lists I thought of a creative solution to the problem that will still allow the automatic search system to be used.
How I envisioned it was a setting like
list.playlistFormats=m4u
By default its blank, so none of the files are considered for playlist status. If its set, then those file formats are read and the final list is adjusted accordingly.
If it doesn't make sense in your grand design, I get it, but if it does, I am sure it will help more people than just me!