Okay, il make this quick. I started working on a mod, but iv run into a wall that only TM2 seems to have.

The opacity of the files, seems to be locked into place unless the file already has transparency.
In TM1 I could edit any file anywhere pretty much and make it as opaque or transparent as I wanted, but in TM2, it seems to ignore this on files that are default opaque. This makes modding significantly more boring since it cant have transparency effects like grating and ect. Instead of displaying it right with see through sections, it fills the area i told it to be transparent. 100% opaque black.

To make sure I wasn't doing anything wrong I went and looked at an original transparent file, like say a fence. and it Still used the old "white = solid, black = hole" So i wasnt doing anything wrong on the alphas.

I can't get TM2 to accept any forced transparency on files that are default 100% solid. Only transparency works on files that are already semi transparent, which is lame.

Is this a common thing and just like bik no longer being supported in signs we cant force transparancy on the TM2 files, or am i just doing it wrong?

no i think you right, alot of things can not be changed like we did with old tm, we having some problems, with a new mod, to be released around christmas sometime, which now may not come,i will post a update here if my friend finds away around it !
Good luck also keep us posted if you crack it please

Gradual transparency levels only work for the RoadRaceGlass.dds and RoadRaceFence.dds I think. Textures which have no alpha channel by default cannot have alpha channels in mods, as you correctly observed.
In a way it makes sense. The blocks in Canyon have a lot more surfaces than the blocks in TM environments. So if you make one texture transparent, some other textures might show through that surface....which would be very weird.

this could also be a feature for ShootMania to discourage people from cheating by modding all the textures to clear and creating chams, since TrackMania and ShootMania both run off ManiaPlanet.

I think this (along with the lack of animated signs) is a victim of the new shadow calculation. TMNF basically had on/off shadows, but TM2 has light reflecting on objects which then reflect light back at other objects. Transparency would mess with it so hard.