I have a couple Malibu Pro Explorers (sit on top) that I rigged for diving. I have never flipped one, although I had a friend start to sink because we forgot to put the drain plug back in. I use the rear well to hold the tank with BC pre-inflated. I run a thick bungee around the handle and valve with a snap link to make sure it stays with yak if I ever flip. I used to bungee across the top of the gear as well as the valve, but I have found that it is overkill as my well is deep enough to not let tank out super easy. I keep the mask and bags, go pro and drinking water in center console. Created a PVC flag pole, and boat sized dive flag to put in the scupper drainage hole near seat. I use the right side strap by the handle to keep the flag pole secure on trip out. I put the flag across the front and under the fins. I usually keep fins up top with another bungee and snap to make sure they can't slide off. I occasionally will throw fins in gator hatch on the way in to get them out of the way. I like having them up top for quick access if needs be. I keep a life vest in gator hatch up front. I tie my lead line to the front handle and interweave the dive flag line holder between the front built in bungee. Overall I am very pleased with my investment on the kayaks. I have made several trips with my wife and friends using both of them. When I go out solo it makes getting to my spots much faster than surface swimming.
The biggest concerns are when the wind kicks up you can get pull around under water pretty good. I have gotten bruises on my biceps by going out after the wind has kicked up. The other part is getting the gear back on the kayak. If your BC has easy emergency dropping of weights I find the tank is much easier to get in if you remove those first and put them in the center console. Then the trick is to use your arm as a fulcrum and put the end of the tank in first. I can usually get it in within 3 tries, and that's a steel 120.
I typically walk the kayak out with my gear on. I bought a set of beach wheels for pulling it that make it much easier to get down to beach. Don't try to pull kayak with gear in it through the beach sand, even with wheels. Heart attack inducing. I also like to keep a waterproof container in the center console with my keys and phone. The perk about having this is you can download any mapping GPS app and have it record your kayak trip so you can see where you have been and estimate where you found the good spots for later.
If you can swing the extra work of hanging it on your car and dragging it to the beach, it certainly makes getting out to good spots more bearable than a 30-45 minute swim. I love it. Just wish I could get out more often.