Could you give some examples and add some details about your setup and why this is a problem for you (e.g. filesystem limitation or viewing/playback issue, and if so, what software are you using)?
That’s probably best left as a option not a permanent feature, perhaps as an option only for special rules, since they can do file/title naming overrides. If it is something specific like “URL decoding detection”, or “unicode character set translation”, then it would help to know the source of your media files that have these special characters routinely that you need MCEBuddy to filter/translate them. MCEBuddy might be able to detect those files and handle the filenames better.
For many people, using the file renaming rules in the profile and the show metadata to calculate a filename for the output file does the job. Are you using this feature?
If it is just one or a handful of shows regularly with this issue, you can use the regex rules in the special overrides to manually rename the shows/media with the funky characters to specifically what you want replaced.