I'm still a very new diver (less than 50 dives at time of writing - all in Roatan) so my dive shop experience is quite limited: a total of two ops.
We got our OW certs at Las Rocas (up at the north end of West Bay beach). Solid shop, great instructor who did a super job working within the time constraints we put on him doing our "resort course", as you put it.
The last three trips we have been diving with Naboo Dive Center. It is connected to a more upscale resort than Las Rocas that my non-diving wife loves being at while we are diving, and we really like how they operate the dive shop (rental equipment in excellent condition, well-organized boats and trips etc), and the DMs/instructors and the boat captains are exactly as you described - fun and personable. Boats are smaller than the Paradise Beach Divers ones, I think. Max 12 divers plus DMs and captain, no more than six divers per DM - and no giant stride, we enter via backroll. West Bay has the advantage (to non cruise visitors, of course) of being farther away from the cruise ports so it is more difficult to coordinate dives with cruise arrival/departure times. Most of the "packing people on a boat" (I think I share your opinion of that) is found on boats from Anthony's Key Resort at Sandy Bay and maybe a couple operators in West End.
Night dives absolutely available from Naboo, weather permitting, minimum four divers required. Prices per dive for all dives are similar to but a bit higher than what PBD advertises on their website (those prices are excellent). "Diving your computer" - once the guide establishes that you actually know how to use it (I'm sure you do, but you probably have noticed there are some divers especially in resort areas that really do not - I have) and gets a feel for your gas consumption they don't come across as nannies. Being totally objective, for the second dive after relatively deep ones to 90-100ft the instruction was "let me know if your NDL drops below 10 minutes" which might come across as "nannying" to some but they
really didn't want us riding our NDL. From observing their interactions with other more experienced divers on previous trips though, that might have been something specific to us since we are still pretty new. If you dive with them, be upfront and honest about your prior experience. They are very professional, and do their utmost to cater to their clients. I think that is true of most shops in West End and West Bay, though - there is a lot of competition.
About cold beer for the boat trip back - for the West Bay operators (and the same applies to West End shops) the dive sites are really close to their departure point. Usually we are tied to the mooring point within 5-10 minutes of pulling out from the beach (or the dock on the south side in some weather conditions) and listening to the dive briefing, then gearing up getting ready to splash. So (from my limited experience) it seems it isn't really a custom there to have drinks on the boat on the way back after the dives. Plus with the boats being small it limits a bit what they can store on them.
Restaurants (I'll stick to West Bay - West End has plenty more options): the food where you are staying was good the last time we were there (December 2023). Bananarama also has a good island vibe food-wise and can easily accomodate a large group (they just move tables around on the sand to match whatever is needed), with live music and karaoke some nights. We love the restaurant at Naboo - the poolside dining there with soft music playing is more our speed. Argentinian Grill is excellent (loved the churrasco last time I was there), so is Beacher's (good lobster specials on Monday and Thursday nights).
Sunset bars - that's much more of a West End thing. West Bay is more of a "sunset dining" vibe. Sundowners at West End is among the most famous, but there are plenty of other good options for that scene. Water taxi between West End and West Bay does not run at night, at least, not officially - I have seen taxis come back to West Bay from West End after dark, but certainly not super late.
Special trips - I've never done one. I hear that the crossing between Roatan and the other two main islands (Utila and Guanaja) can be a little rough - but since you are a boat owner from the NY area you are likely accustomed to much more severe conditions than what the Caribbean usually has to offer and my idea of rough might just make you laugh! If I were to choose one of those trips, I would probably pick Guanaja - just because it would be a great way to see the entire north side of Roatan and the diving there, at least according to a trip report here on SB from February 2023, is reportedly spectacular. Worth the cost? Since the Guanaja excursion does include two tanks which from West Bay Divers is around $100 right there, fuel is very expensive here, breakfast and lunch is included and the wine and beer
is also included on the boat trip back
, it could very well be.
Sorry, this has turned out longer than I meant it to be - not uncommon for me on ScubaBoard. I hope some of this information is useful to you.