@Puffling it has been a few years since I have dove with SC, so please take my answer with a grain of salt as things might have changed since my last visit.
IIRC, you will have time after you surface from your last dive until the boat pulls into the dock to pack your gear into your boat bag and get everything sorted out. By the time the boat gets back to the dock, you will most likely be able to pick up your boat bag & leave the boat. The hotel shuttles run on a relatively flexible schedule so the boats will make every reasonable effort to ensure that they are not going to back their customers into a corner. The shuttles are also operated by SC, so they will not leave until everyone is there.
In the past, I have found that I typically had time to get off the boat, and hang out in the dive shop for a little while before I had to go to the pick up spot for the shuttles. The whole system is set up to make your life as easy as they can, while still meeting their needs.
I do not remember any storage at the site, but again, it has been several years since I have dove there and they might have storage now. On that, hopefully someone who has been there recently may be able to answer, or perhaps you could contact SC directly with that question. I think that you take your gear home with you every day.
As for how I found the return journey ... I was on a bus that was full of people who were thrilled with what a great day of diving they had. Everybody was upbeat and in a good mood. The driver will eventually get to your hotel and you get off and say goodbye to all your new friends. It was very easy.
I hope that this has answered some of your questions. I would highly recommend using their shuttle. I don't think that there really are any better options.