It could be estimated that a big part of users would rather refrain from shutting any apps while doing periodical backups (for obvious practical reasons) - as opposed to shutting apps when having intention to shutdown, therefore coupling such a feature with exittc sounds like a half-baked solution.
Personally I have never have any issue with restoring a backup which was taken with apps running, but I could imagine that an inclusion of pid- or lock-files could possibly create such, perhaps you could make an attempt at looking into which file(s) is causing the problem and then add it to .xfiletool.lst
A different approach could be to include something like 'killall [-SIG] process-name' in filetool.sh at the beginning (or use a wrapper script with something along the lines of 'killall midori && filetool.sh -b').