Hi utfz.chris.ke,
We just released version 2020.1.3 today, which should solve this issue with fully transparent areas! It should now work without you having to change your workflow at all, but if you’re interested about the technical details, I explained them in this post. Also, check out the release notes on the Texture Tools Exporter main page to see what else has changed in this version.
Thanks again, and hope this helps!