As you know Upspring doesn't support transparency at all, there's no way to do it. For those of us that still rely on Upspring to create our Texture1 and Texture2, this is annoying. But no fear! We can trick Upspring. Note: I'm well aware there are much better ways to do it. Stfu.
Step 1:
Create your Texture2 without transparency; load your Reflection map and Self-Illumination map and save it as something.
Step 2:
Go back to the Texture 1 creation tab. Load your just-made Texture2 (without transparency) as "Color texture", and then load your Transparency map as "Team color" -- teamcolor in Spring is simply the alpha channel of texture1 so it will simply attach whatever's there as the alpha of "Color texture", in this case we're tricking it to attach our transparency map as the alpha of what is actually our texture 2 (it keeps both of those layers intact). Save it as whatever you want your final Texture2 to be called, and voila, you're done.