OK, I'll be the dissenting opinion and say that in THEORY I would take it there for the following reasons:
1. Clutch replacements aren't rocket science - heck clutch technology in general hasn't changed much in a hundred or so years (OK, the throwout bearing are usually hydraulic now and some clutches are dual mass).
2. Pep Boys is generally not so good for diagnosis and better at parts swapping (true for a lot of shops really)
3. The clutch is a Luk unit - decent brand used by lots of folks on this board and others.
Having said all that. Here are some downsides
1. Ad is for clutches up to $275...the M5 unit lists for $314 on their website so you'll be on the hook for the additional $39 dollars - no biggie.
2. Does not include a new flywheel or flywheel refinishing. BMW now charges an INSANE amount for a new flywheel - $1300+ - and Pep Boys doesn't even show to carry it. Pelican Parts lists a Luk flywheel for $775. If your car needs a refinish or new one - you could be in trouble here - when you are working on your own car that's one thing, but when a shop is halfway into the job you can be sort of held hostage in these situations (not true for just Pep Boys obviously).
3. The BMW vs. Pep Boys Factor - invariably, Pep Boys will come up with some excuse for why they can't do your car. As an example, I couldn't get my wife's car aligned by them or various suspension parts replaced because of the "special BMW requirements". In the case of the suspension parts that meant: tighten the bolts with a loaded suspension and X lbs of weight in the seats, trunk, etc (all of which can essentially be done with some bodies in the car simulating this - which is ironic because the weights are in fact simulating bodies).
Anyway, my guess is that if you take it to them they will tell you outright they can't do it OR will give you some excuse part way into the job as to why they can't do it or complete it.
perhaps; but, i'd still be willing to bet 50% of them throw it out and remove the self-adjusting mechanism, just like high-volume glass installers remove all the spacer blocks from E39 windsheilds because they think they're just packaging.