3coolcats, that's an excellent question. I think you should email the Penn admissions office and tell them you are very interested in attending the engineering school at Penn. Tell them you want to participate in the QB program and ask if, given your specific interest in engineering, you should only apply to Penn during the Regular Decision round of the program or if there is a way to apply specifically to Penn engineering only during the College Match round.
Do keep a positive tone throughout your email. Just ask the question without saying anything like it seeming unfair.
Given your interest in only the engineering program, you may not want to put down Penn for the College Match round. (But find out from them if somehow specifying only engineering is possible.) I do think it is worthwhile for you to still apply to QB. Those fee waivers are very helpful. You could always opt not to do the College Match round and just do RD, depending on what schools you're interested in, what response you get from Penn, and just where they rank in your choice of schools.