If it's listed on your transcript then it will be factored into your overall and BCPM gpa calculations by AMCAS.
Also, FWIW if you're doing that level of for-credit research, you'd better have a LOR from your PI in your packet somewhere. If yes, it likely will not be seen as fluff. If not...well, it wouldn't bode well to have worked with someone one-on-one that much and have them not recommend you. Though from what you've said, it doesn't sound like that would be an issue for you.