Before I just started to do everything through wine, I used rockerbacon's MO2 scripts, which seems to have since been succeeded by MO2-LINT. Seems like a decent option for what you're looking for. Otherwise I guess you could install MO2 some other way and make a shortcut in your game directory called 'Fallout3Launcher.exe', or 'Fallout4Launcher.exe' and so on.
I've used MO2.
However, I have to say that the most-convenient way I've used with Bethesda games, if you're going to start with a modlist from Wabbajack, is to use Jackify.
https://github.com/Omni-guides/Jackify
It'll set up MO2, create a new, modded Steam entry for the modlist (so, like, it won't fiddle with your vanilla game install), pull down and set up the associated mods in the correct order, and you can fiddle with said modlist in MO2 after installation.
If what you want is "game with modern updates and then maybe a few particular custom changes that I want", I'd say that that is easily the most painless route in 2026.
I just stumbled upon this post in my hone feed and knew that I would probably be needing the answer myself some day and now I know. Thank you!
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