I have a question about linking accounts.

Is there any way to link my account to my Steam without having to unpack my Xbox One or reinstall the Windows Store version? The WS version is practically malware, I had to dig through my registry to clear out the space last time and I'm not doing that again just to link it to the better platform, and my Xbox One is currently packed away.

No, you are required to login to the other platform and get a code to link it.

Only way I heard was people using the PSO2 Tweaker from Arks-Layer to do 1 installation for both MS Store and Steam version.

I don't use the Tweaker anymore so not sure how it works anymore.