i did a quick check on the textures. as far as i can tell only the logo is missing transparency. plants, space debris and glass have a working alpha channel.
as for the blinking lights, that seems to be model related. after removing your mod i got the old textures, and the old lights were blinking in black squares too.
wikipedia has some interesting articles about
dds and
dxtn.
png is the only lossless widespread picture compression i know. but when packing multiple files with similar content, your tools of choice should be 7zip or winrar, due to solid block compression.
Threaded Mode