I had noticed the version number. The latest official version is 1.6.1820. "GOG 0.1" hints at something GOG-internal, while I have no idea what the insertion of "0" (1.6."0".1820) could mean.
But do you know when this new version was released? As far as I'm concerned, it could have been there for quite some time (I haven't downloaded Morrowind for a number of years, but I do check the list of updated games every now and then, and can't remember having seen it in this list). And, to be honest, I have no intention to install the file just to be able to check dates.
That ini and resolution were reverted back to default is what I would have expected. The download file is the full game, and not a patch, so it would simply overwrite everything, including the ini and the registry content (resolution) of Morrowind. Instead of running MGE XE again, you could also have edited the registry (not advised for people who are not familiar with editing the registry), or used the Morrowind Code Patch (MCP).
But I can't say what else a new Morrowind installation would mean for modded Morrowind (depends on the mods, I suppose). It may well have caused the warnings mentioned in the original post - because mod content was overwritten by the new installation. I'd strongly recommend to at least check, or better re-install all mods after a full installation, and re-run utilities like MGE XE and MCP.
I don't use Galaxy, but I recommend to all Galaxy users to disable automatic updating for Morrowind. If an update is offered, check for information what it does (don't expect Morrowind itself to change).
If a player decides to update the game (Galaxy or direct download version), be prepared to re-install and re-activate ALL mods, or accept and resolve issues (for example, savegame warnings or even crashes when loading a savegame - crashes when starting a new game would be highly unlikely for the updated, but then unchanged game).
It's impossible to be more specific. Just work on the assumption that every file of the original Morrowind installation, which was verwritten by a mod, will be reverted back to the original file. When you start the updated Morrowind game, it's more or less like starting the original unmodded file.