I'd recommend writing a good cover letter explaining what you said above. If you can throw out the correct buzzwords to get an interview you'll have your chance to shine. It will be quite evident whether or not you know your stuff. Since QA is process driven, those processes matter more than specific testing software. Remember, monkeys can be trained to push buttons.
BTW, I always appreciate QA folks who can think outside the box and think like the customer. Too many times test plans are put into place by Development....whom have a vested interest in stuff passing QA.