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I generally prefer to manually install and update my own mods so I've never tried running a mod manager in Lutris, but generally the thing you want to be mindful of is if you have everything running in the same wine prefix that needs to interact with each other. Each wine prefix is kinda isolated from another, so when you change which wine version (and therefore prefix) launches a given software, it loses all of its stored data from the appdata folder because that was left in the old prefix