That's been my experience also, the LDS trips always cost more. We always book our own trips now. We have two shops in town that have dive-travel agencies on site - even giving them our exact dates and desired locations, they were never able to get within $200 of the prices I found using a combination of resort and airlines websites. Often it was a lot more.
On the LDS trips I think it's partly because you're all paying so that the staff person from the shop goes free. I know several DM's/Instructors at one shop and they never pay since they're "working" during the trip.
Although it's a profit maker for the LDS also.
We have one shop that books a liveaboard annually, I looked into booking the same boat for my friends, the quoted price for 12 of us was $14K or $1166pp. They even have a graduated payment schedule so it's $1000 down with increasing payments due at 6, 4, and 2 months prior. So there's no big up-front payment commitment required - by the LDS or privately. The LDS trip also includes r/t air and 1 night in a hotel.
Since it's a liveaboard, there are no other costs to the LDS. Next month r/t air from here would be $429 at retail. Even if you add $100/nt pp for the room. the total is $1695 pp. And I'm not getting any wholesale discounts.
The LDS charges $2495 for the same trip.
Surprisingly someone I know slightly just went on the trip. When I asked why, he said that the convenience of just showing up was worth it. I can go to Coz for a week air/hotel for the $800 difference so I'll do the work.
We have a small group of 8-10 that travel together regularly, the last 5 years we've done a spring trip to somewhere warm. We do all the booking ourselves - two of us will typically find the best deals and options - redeye vs. overnight etc. and let everyone decide/book their own itinerary. We always reference the name of our group when booking, that's twice given us discounts at the destination diveop since we were pretty much their business for the week. We do as many dives as possible typically - sometimes with a day break in the middle of the week.
We always save money over anyone's published deals although a couple of times, the national dive travel agencies have been really competitive with a group of our size. I often give Caradonna, Aquadreams etc. a chance at our business - and call/contact resorts directly. One time that resulted in a condo upgrade at no cost that the dive travel agent didn't know about.
So you might try something similar in your area. We have a non-LDS affiliated club that meets monthly. And a private forum here on SB. There are about 200+ registered members in the club but only about 5% are active in our local or travel activities.