brent_hamel , QuaziGNRLnose
Okay I found a fix.
In the runtime.js of the Q3D Model, on line 3796 there is a typo;
this.mat.alphatest = alphatest;
It should be a capital T, like so;
this.mat.alphaTest = alphatest;
I also re-enabled the action in edittime.js on line 244;
Then I used the action to set the alphatest value to 0.5 on the model
I also set the transparency OFF as well on the model.
This should fix your issue brent_hamel
Apparently judging by this comment in the edittime on line 241;
// these two weren't really having any effect in webgl renderer, so they're deprecated
You must have overlooked a typo, QuaziGNRLnose , which is why it appeared not to be having any effect.
So if you fix the typo it will work again.