The producer way overcompensated for the natural tone of the UV by overdubbing 6's and tweaking the crap out of the mids and high mids.
Remember back then the rock 7 string was a new commodity and not very well understood nor accepted. The producer tried to make the 7 string "sound" more like a six string and that only accentuated the worst tonal characteristics (imho only) of the basswood+blaze+7+Vai's naturally wiry tone anyway.
the producer/engineer was Vai himself, he took home all of the masters and remixed it. (I know the booklet mentions Mike Clink, producer) If you don't like his tone, so be it, but don't blame someone else...What really messes up Vai's tone is the keyboard overdubs and overusing the Eventide though.
IMHO the guitar tone on SOTT (1989) isn't bad at all, just compare it to "...And justice for all" (1988 ) or to Queenryche's "Empire" (1990 best I can
has rubbish tone, on jet city woman
It's just the way things were back then. Producers and Engineers were just getting to grips with the transition form analogue to digital, anything produced between ca 1987 and 1992 suffers from this.
Compare "...justice" to "the black album" (1991) or "rust in peace" (1990) to "countdown to extinction" (1992) or "appetite" (1987) to "illusion" (1991)
All of the earlier examples sound like the guitars were recorded in a small bathroom.
Just for reference, EvH said the first VH album mixed properly and correctly was "Balance" (1995!), he did most of it going back and forth to his Mercedes, in stead of listening to the studio monitors