You can add them if you'd like. I usually prefer categories that actually finish the game, but if you think you're going to care about all these categories and push them, then go for it. If you're going to do a couple runs and stop, maybe not :)

Sure, I never like verifying my own runs so I'd be happy to get some help :)

I definitely agree with 3rd party tools. for the lower left double money, for Any% i'd lean towards leaving it in. It's part of the game, I'll chat with some other mods from similar games and see how they feel about it.

Mother brain room is the hardest room in the game to learn. I imagine both tutorials go through it but I'm on my phone and can't check.

If you have specific questions about it, I'd join the discord and ask there. Discord link should be on the menu to the left. There are many many active runners in there who can help :)

I would click on Guides to the left, and check out either Mazimov's All bosses or Yogi's 2 boss tutorial (they're the same category--All Bosses). It's a great jumping in point for Metroid to start learning!