Keep in mind that the issue is with ComSkip, not MediaPortal. In so far as ComSkip can't handle the split file situation and MediaPortal's TV Engine (2) isn't going to be changed (assuming it could be changed).
If ComSkip gets fixed then MediaPortal won't need any changes. If the feature was disabled in MediaPortal we'd need to set it back when/if ComSkip gets fixed.
Either way, until ComSkip is "fixed" it wont work with manual recordings, so the way I see it there is no reason to change the way MediaPortal handles Manual recordings.
I think erik will need a sample set of files, but I haven't been able to create a sample for him because I don't have a TV Engine 2 setup running at the moment. Perhaps another user could help out here?