It could be that the "hi-z" input of the interface isn't high z enough. What kind of pickups does the guitar have?
What? I mean, you usually seem to know what you're talking about, but I just don't...???
What is likely is that interface (like most) adds gain to its instrument inputs based on the assumption that guitars and basses are significantly lower than line level, and ends up (like most) adding too much gain for some very loud instruments.
What is also likely is that the other interface was also clipping, and by turning down the software mixer, just turned down the already distorted signal.
If this is a passive guitar, you could put a buffer (like a Boss pedal turned off) between the guitar and one of the line inputs and then actually record much cleaner signal. If it's an active guitar, it's already buffered, so you can go
straight into the line in. In either case, you could just turn the V pot down at the guitar like you said, but on passive guitars the V pot always also affects tone.
Or you could just go with it. Attenuate the signal either in InputFX or just the normal FX slots. If you're just going to distort the signal further (with amp sim or whatever), then it's really not that big of a deal. Not "best practice", but not the end of
the world. The distortion itself never bothered you before!