
I am really not aware of the technical difficulties, since I've never tried to learn how hardware-accelerated engines works. All that's needed is to draw both the lighting and the liquids in a single pass, using turbulent projection for the liquid texture and regular projection for the lighting, and combining them together before blending them into the framebuffer.
Support in mapping tools is almost there. The latest TyrUtils needs liquid brushes to be compiled as func_detail with _dirt -1, but hopefully this won't be needed anymore in the next versions.
I remember Spike saying that FTEQW also supports this, but several other engines would also need this feature.