So... a large grain of salt with what I write, as I am new to using SX Pro myself.
By "INNER STORAGE" I think you are referring to the system storage, and NOT the SD card storage. So... if you are indeed reffering to the system storage, for #1, I don't have a factual answer I can provide you with. I should note that some games, like BotW, use a lot of space for their save game data, which is on the System Memory. But to what degree this could be an available space problem for you, I don't know.
For #2 I can provide a couple of thoughts:
A. The SX OS CFW should be on your SD card and NOT on your System Memory. So anything that you do to your system memory should not affect your SD card's used memory. However, thinking about it, if you format / reset your system memory, account association to any Nintendo games on your SD card may need to be reassociated or redownloaded with your Nintendo Account. I imagine that any of your homebrew files, since they get placed on the SD card as well, should be safe also. Really, what I would do is remove my SD card before any factory resets on the switch.
B. I am not 100% sure about this, as I believe the AUTO RCM feature starts off of the SD card information. I think you could test my hypothesis by removing the SD card off your system and power-cycling your switch... it should go to a black screen if the Auto RCM is still programmed to run without the SD card or dongle inserted. If Auto RCM isn't, then it should go through the OFW start up like normal.
If you don't mean System Storage with 'inner storage', then just ignore my response.