I'm wondering if: The notification dialog is really necessary? (eg. could it just force the rejection and log a status message)
Well, only you know if its an error with the timestamp, or something "touch"ed the file without changing it, or you edited the file with __ANOTHER__ editor (gasps of horror at such infidelity ;-), the plugin can't tell, so it asks you.
IIRC the discussion at the time saving bookmarks and folds was contentious because if the file was changed they won't be in the same place. So the modification check was used to reduce that risk.
Better that you find why you get timestamp mismatches. If something touches the file just don't do that. If its an error in the timestamp there are several possible causes. Depending on the OS and the filesystem the timestamp may not be updated immediately after the file is saved, so the value the plugin reads is the previous time it was saved. This is particularly likely for remote filesystems.