Usually COMLEX scores are not listed on your medical school transcript nor Dean's Letter. You still need to pay the $50 transcript fee. Every residency program requires an official transcript to be sent, normally through ERAS.
It is indeed necessary. The programs will need the "official" score. In the long run $50 doesn't mean much. I spent over 2-3k during the interview season (applied to 40+ programs). ANd I ended up matchign at my #1 choice which didn't even go through ERAS! Ahhhhhhhhhhhh.............
I matched through ERAS, although I did have a few programs hint at offering a spot outside the match. I actually asked my PD if he'd sign me outside the match (so I could go ahead and start looking to buy a condo, etc), he declined, saying he didn't want to mess anything up with the NRMP since it was our first year.