I don't think there are any easy answers for you.
Personally, for me this is what I do and haven't "yet" been banned "though I assume at some point I might".
I use my hackable switch to boot into legit firmware and download my purchased games from the Nintendo shop. I then go into airplane mode and reboot into custom firmware to play my legit games while using the cheat feature to run whatever
cheats I want for the game then save the game with the
cheats I want applied to it. Then reboot into stock firmware, go back online and let the cloud save feature upload my modded save file. Then I load my pure stock patched switch which I use for me every day gamming and download my save file from my modded Switch.
So far I haven't gotten a ban "though I assume the full risk if I do end up banned".
So in short, you may or may not get banned, but life is short, enjoy your console and what will be, will be.