So for the latch, obviously what you did is important

But here's some more useful info:
https://jetboaters.net/threads/engine-compartment-keeps-opening.15981/post-387358
Further to that, some people can't seem to get that latch to stay latched. Probably due to variabilities in the boat builds, latch install, etc. Two other things to consider if it keeps happening. One, replace the two springs with weaker ones. The ratings are on there with stickers, just buy the same ones but with less power and figure out what makes the hatch "neutral". Mine is like this now and I just have to apply a small amount of upward pressure to make it go up.
Another option is to get rubber latches like they have on coolers. But that may not be as nice looking.
If you're talking about the gel coat roughness, gel coat can definitely be polished like a car. In fact, it's way tougher than a car. Compounds like you're used to for cars will work just fine on the fiberglass gel coat. You can even wet sand it if needed. So just like any other rough surface, start with a coarser grit and work your way up to a fine grit. You can polish it to a mirror shine. By hand works, but obviously requires elbow grease.
Scratches can often be buffed out fairly well with a buffer and compound again. Just be careful... it's WAY less likely to burn it like a car paint, but it still CAN burn if you stay on there too long or apply too much pressure. If you go slowly though, you can definitely polish out scratches. Again, sanding works too if needed. I had a fairly big one on the port gunwale, sanded and polished it out completely. But it took some work.
50 psi is correct. Your trailer should have a sticker on the tongue area with these details. Look there. But 50 psi is correct for your trailer.
If you have any other questions, ping me. I can't promise I know all the things, but I am quite familiar with your boat.
Before you make one of these common newbie mistakes, here are a few things:
1. NEVER try to remove the grate under the boat. It is NOT designed to be removed even if it has bolt heads there. If you try, you will break the sealant under the engine on the other end of those bolts to prevent water from leaking in. Scarab really should make these different somehow to avoid this. If you need access to the pump, access from the rear is simple and easy to do. Takes about 15 min with simple tools once you know how to do it. I can help if that ever happens.
2. Your carbon seal prevents water from getting into your hull. It is located around your drive shaft where it exits the hull. It is ONLY cooled when the boat is actually sitting in water. No other procedure cools it unless you do specific things like spray constant water at it from under the boat. So, you should never run the boat out of water for more than 2 min (official number), but almost all of us never run it for more than 60 seconds (better). Even for doing oil changes, etc.
3. When running the engine out of water for say more than 15 seconds, you should cool the exhaust system. To do so, you need to use that flushing port. The procedure order is IMPORTANT. Engine on, water on, water off, engine off. In that order. In essence, never water pressure unless your engine is running. Otherwise, water can work its way up the exhaust system into your engine. Don't be my uncle that did that recently on his Sea-Doo. lol
4. Read the manuals. Both of them. The more important one IMO is the BRP Operator's Manual:
https://www.operatorsguides.brp.com/ Select Rotax>JPS>two letter code representing year starting at AA=2014>Engine HP. The other is the Scarab manual:
Scarab Jet Boats | Owners
5. Don't forget to enjoy the boat! lol