These seem like bugs that could be fixed, but it also seems like there should be relatively simple ways to work around them without disabling about:config, e.g.:
If some settings can cause a crash (and you don't have a complete list), create a separate launcher that only edits the settings in about:config without ever trying to run other Fenix code, so the user always has a way to revert settings if they're causing a crash on startup.
If some settings can be applied but are reset the next time the app runs, save the setting value itself and then re-apply it on each startup.
Other problems like settings doing nothing or breaking websites are just ordinary bugs. Until they're fixed, the user can just refrain from using those settings, or revert them if they cause problems. These sorts of issues are acceptable for users knowingly mucking around in about:config, it's fine, fix the bugs when you get time. It's no reason to disable access to the other settings that actually work in the meantime.