When there are different versions of a work, there are usually multiple different works on MusicBrainz as well, with a disambiguation comment specifying which version. So you can link the recording to one of those if your release mentions which version is performed (you may have to create those works of course). There is also usually a “catch-all for arrangements” work, which you can use if you don’t know which version is performed. But I wouldn’t guess which version is performed. Unless there are some major differences that are very apparent, like one version having different parts, but that is the only reliable way if you can’t find a reliable source mentioning the version.
Pictures at an Exhibition is a good example of this practice.