To avoid scraping your clearcoat, you could use a plastic applicator to scrape.. If you use a heat gun/hair dryer and consentrate the heat to behind the moulding, that will help also. Just dont hold it close or for a long extended amount of time. Thats what we use at work, always does the trick... The reason for a difference in colour could be the door/s where painted before and they just masked off the rubber moulding.. Or it could be the lack of sun its seen, meaning the door's paint has broken down quicker. Try a cut n polish, it 'might' fix it or at least make it less noticable..
If you wet rub it with some 2000, it will only fix it if it hasn't been painted before. (Meanin the clours are different and no polish will fix that)
Hope that helps too.