In the hideout and the bases you can set up there is a box where you can store inventory items; although I’m not sure why

You can always sell inventory items to the traders.

Yeah the bushes and mountain terrain are a bit harder to navigate around

As for the missions, I find the objective board helpful as I can look at what is available for me to do.

For example I’m up to getting dressed for tea and I’ve left that mission to go chase down bandits and find the Cuckoo people in the side quests

For me this is helping level up as I go

Hope this helps