Okay, so I assumed you'd been having problems building your latest RUGCD release, so I extracted the contents of the new ISO and rebuilt using ISOCD-Win and sure enough it wouldn't boot. Upon investigation the code had two bugs.
The first was an encoding issue where it was using UTF8 instead of ISO-8859-1 which was causing some filenames on your CD to have multi-byte names (e.g. for anything containing ³² like CannonFodder CD³².info) and thus knocking out the size and alignment calculations.
The second was a sector alignment problem that was not correctly preventing directory entries from crossing a sector boundary in all cases.
Anyway, both issues are now fixed and I can create a working CD from your RUGCD files using both CD32.TM or CDTV.TM. This version also has saved configs and the ability to abort during the build process as you quite rightly suggested as being useful. It also has the ISOCD CDFS stuff implemented. The only thing missing from your list is batch support, which I plan to add in the next version.
The new version can be grabbed from my folder on the file server or here:
https://www.dropbox.com/s/mofoo1i21n...n-1.2.zip?dl=0