I have been looking into this and the behaviour you are noting is apparent, though I believe this may be related to EAB calculating the applicable Unicode blocks for a given input font, and as such is an indication that you may want to review the input character set as the new font might not these characters.
Well, the "Input Character" file is there to limit the glyphs of a font to the desired subset, not to wish glyphs into existing. :-)
So I would say that is more likely that someone needs to convert a bunch of different fonts to the same subset of glyphs as it is
that the different fonts need to be converted for different sets of glyphs.
And even when someone needs to change the "Input Character" file for every font, this does not require any more clicks than with the current implementation while everyone who does not need to change the "Input Character" file must select the same file again and again.
Even only browsing thru fonts to find one that has all the glyphs needed for the selected set or looks ok for the selected set is
a tiny bit more cumbersome now.
And yeah, I am having fun here "complaining" over this first-world useability issue as I have not found anything more serious so far - good job! :-)