what exactly is your question? can you have transparency in your texture? sure. You don't "need" to do the whole setting opacity to .8 in the node in the .mat which the .mat exporter will do automatically for you, you can just change the opacity of a layer in a program like photoshop, and have various regions of it be transparent, while other parts are completely solid, works just as well.

hmmm, ok. so, since the .mat file exporter doesn't pick up any texture with the "glass" label in it, just the shading values, then what i'd have to do, if i were using the .mat exporter, is name the object and texture something else, and then go back in with the utf editor and add the transparencies manually?

reread the instructions on the mat exporter, if you use the word "GLASS" anywhere in the name of the material, it WILL give it a set opacity of .8 in freelancer. BUT, rather then having an entire material be given the same opacity, you can just set various layers in photoshop to have transparency, and then just use that as just a normal texture without any editing of the .mat. Freelancer will / can use targas or direct draw files with transparency in them... I meanm just try it, it's pretty straight forward...