I have no direct experience with that dive op, but we've stayed at the El Prez several times (love the hotel very much), and watched them (Scuba Du) come and go. As I recall, their boat looked huge (that is NOT a good sign: giant boat usually means too many divers in the water with you, ie a "cattle boat"...you do not want that). Honestly, I've never really heard much about this dive op one way or another, certainly there's no frequent praise or rabid following here. AFAICT, it's just your standard resort operation (which is to say, maybe adequate, but probably not outstanding).
I think what generally passes for wisdom/learned experience from members here is, regardless of where you are staying, just pick a great operator (that usually means ignoring the hotel's dive op). We always dive with Jeremy and his boutique dive op "Living Underwater." Have been using them for years, they're awesome.
Unless something has changed (and I doubt it has), your dive op of choice can just stop by the hotel's dock to pick you up/drop you off every day, it's no big deal for them, and super-convenient for you. That's what we've always done, it's a non-issue. It's a common expectation at almost every hotel that divers use their favorite op, you do NOT need to use the hotel's house op (only a few actively work against their guests and independent dive operators, shame on them).
You've picked a lovely hotel. Why not pick a great dive op, too? Just my 2 pesos.