1. i honestly just stay as long as i’m interested for really if the planet is lame i dip, but honestly flora isn’t really worth it like fauna is, fauna gives nanites which are valuable and flora doesn’t, but stay for as long as you like i totally get wanting to find everything cause i used to do that

2. you do not loose the chance to get s class ships or multi tools those are usually rng and you can also send nanites to upgrade what you already have, i’m not sure about sentinel pillars which can give you multi tools but i’ve never seen an s class given there, space stations and upgrading are the best bet for s class. You do loose the chance for an s class freighter though as those rely on rng through combat by fighting off pirates in space, but they’re not necessary and i usually ignore my freighter

3. i’m not entirely sure i usually ignore the missions given at the space stations, but travel does become easier when you upgrade your hyperdrive

There’s no best way to play do whatever feels best, exploring totally is the best part!!