Solid take, in my experience the photoshop way is a work around to be honest for forcing .TGA files to have the alpha channel (since the exporting is treated completely different if it is .PNG or .TGA there).
The main issue with this though is that sometimes, especially video games, control over the colors where the alpha is zero (or “fully” transparent) is required (premultiplied alpha blending workflows for example). At this point I think it’s better to use something else, .PNG and transparency of the layers (or globally making one like rasterizing to mask with a layer at the very top) works perfectly fine for UI-like assets. For intricate R-G-B-A handling I’m just using substance designer when possible in the end (which also has another set of constraints, like textures there are always power of 2, sometimes a positive, sometimes a drawback).