While I agree with you in principle, Engineering classes definately ARE NOT BCPM as far as AMCAS goes. Many threads on that over the past couple months.
Now, will a school accept an engineering rec as a science rec? Only 1 answer: CALL THEM. You won't get the right answer on SDN, and I'm sure this is important enough to spend the 5 minutes to find out. Oh, and I would do this to all schools you are applying to. You don't want to be out 30 bucks for AMCAS, 50-100 bucks for a secondary, and whatever in time becuase they don't 'accept' your letter. I'm sure they are not all the same, so you probably want to call each one. Let us know what they say
-chop