That is strange, I cannot reproduce it. The problem was that the checkbox was not editable and could not be checked for any songs with missing naming tags (like it is not editable to be checked for duplicates) regardless if the relative option was enabled. Also in the one time that I proceed with it, it placed in Music Library files that were not reorganized (if I remember correctly it happened for every file, also for duplicates but I'm not 100% sure, might have been only for the files with missing tags). I think I have even restarted MusicBee and continued to have that issue with not editable checkbox...
Is it possible some error/exception ended up to such a behavior? At the same time I remember I attempted to use Auto tag by album for one song but Title was added at the Artist tag and vice versa (returned to correct behavior after restart). It was the same time that I was trying to use brackets on the role field of a 2nd Artist on a song. I tried to repeat those steps but again couldn't reproduce that issue. I have started to reorganize my library with small steps and it seems to work as expected.
I'll be more careful and double check before posting something as a bug report in the future...
About files placed at Music node, it does happen for files with missing naming tags even if the option to not reorganize them is selected.
Also one other thing I noticed is that if there are more than one files with the same naming tags, some of them are not reorganized since a file with that filename already had been created from reorganizing one of them, but at the file organize window the error messages for these failures are placed on randomly chosen files not for those that were not reorganized
Filename Char mapping seems to not work for me, I cannot type anything on any of the replacement fields
Best regards