I have played since NS was released. Listen to me.
When the model becomes transparent, you can see through it BUT its like clear tinted glass, slightly tinted by the skin of the model. if you had a glass sphere tinted slightly green, the edges which cross over closer to the other edges are less transparent as the tint stacks up.
Attached is a TINY 4kb image demonstrating.
For an experiment, try getting some of that see-thru tinted paper and place another piece on it. The colour will darken.
In this manner, if you look closely you can make out the OUTLINE of the model, as the edging is darker than the body. This also makes the walls seem to 'bump out' when you look at them, giving the alien away, but only if you look very close.
Even knowing this, unless you know the alien is in the room, you need a keen eye to spot them. Some people are like me, and are just talented. Must have been all those "Where's Wally?" books i read as a kid...

I have been banned once myself for your kind of "hack" you describe. It ended up with the admin losing his priveledges, as it was secretly my server. So watch what you say.