Bad water transparency layering in start level
In the start level (using the rerelease basedir), if you look at the water before episode 4, you can see that specific sections of the bottom surface incorrectly render over specific sections of the top surface. (Specifically, lower surface's far-left corner renders over any part of the upper surface, and the rest of the lower surface's left two-thirds renders over everything in the upper surface except for a section on the near-left.)

Related: https://github.com/Novum/vkQuake/issues/656. I thought this was vkQuake specific at first but guess not. This issue does show up slightly differently between the two ports though.
@ericwa, @andrei-drexler, @Novum ?
P.S.: Have you bisected this?
It's been in each version I've tested so far, including 0.94.4 (2022-05-14).
It's possible that it was introduced between 0.93.1 and 0.94.x when re-release support patches went in.
Note that this is specifically in the re-release's version of the start map, which has transparent water unlike the original, so it might be that this never worked.
Vispatch'ed id1 looks OK to me? (i686 linux, qs from today's git, both with r_wateralpha 0.4)
ID1 1.06 + vispatch:

ID1 - rerelease:

I've also spotted this issue in QS (and vkQuake) in some other levels like Dwell v2.2 (s2.sav.zip):

I did notice that Ironwail does not have this issue. I search its issue tracker and found this post https://github.com/andrei-drexler/ironwail/issues/139#issuecomment-1271947987 explaining their solution.