"alpha" "1" is supposed to force the entity alpha to 1.0, even if it has water polygons. Here is the description from fitzquake's readme:
added support for per-entity alpha, and it works even without a custom progs.dat, works on static entities too, and both bsp and mdl models. Set values directly in the map and/or control it with quakec. When setting alpha, a value of "0" is interpreted as "default", which means 1.0 for most things, but for water polygons it t means obey the value of r_waterwarp. A value greater than 0, up to 1.0, will explicitly set the alpha, and override r_wateralpha for water polygons. A value of -1 will explictly set the alpha to 0 (invisible), and override r_wateralpha. (requires the new protocol, except for alpha -1, which makes things invisible even with protocol 15)
"alpha" "1" is supposed to force the entity alpha to 1.0, even if it has water polygons. Here is the description from fitzquake's readme:
(from: http://www.celephais.net/fitzquake/files/fitzquake085.txt )
Test map: alpha1.zip . Water alpha is set to 0.5 in worldspawn, the func_wall on the left overrides alpha to 1.0 and should be opaque.
quakespasm 0.93.0:
result with 0.93.1ish aka r10:
In case it helps, this doesn't happen with static ents (changing the func_wall to func_illusionary works around the bug).