so, I literally just made an account to say this, and I don't know the forum too well. if this is in the wrong spot, feel free to tell me off for it.
on to my solution. this warning:
Warning:Changing settings in the Skyrim Launcher can undo user-configured INI tweaks. Steam has also been known to update the INIs under certain conditions. This does not apply to MO users except if running the Skyrim Launcher or Steam from within MO. To avoid "unapproved" alterations to the default configuration files, it is possible to set the INI files as "read only" after all the tweaks are in place. Do not set the MO profile INIs to read-only since this will cause problems.
is entirely valid and quite frustrating, particularly if you are like me and spent an hour or so editing your .ini files. but if you needed to, say, change steam mods with the launcher, or perhaps fix the certificate error thing with TES5edit, the launcher will overwrite whatever you've done.
however, I've found you can easily save your work by copying your ini files somewhere else, running the launcher, and then pasting them back in again and overwriting the new ones. this way, you can stop worrying about running the launcher without messing around with read-only settings and what not. the certificate problem is solved with no issue by doing this.
honestly, because of the benefit those .ini tweaks give to the game and the sheer amount there is to change, it can be discouraging to see that warning. thus, I humbly suggest that someone add my caveat to the warning.