Hi dmarker22,
Thanks for your message.
You are right, as mentioned in Unwanted discard of colors when alpha is zero - #7 by AlejandroC it is a known issue and present in the latest PVRTexTool release. The last PVRTexTool release where this issue is not present is v4.23 from the 2019.2 release.
You can find the installer in our Developer Portal (under Previous Releases - Imagination Developers → PowerVR Offline Installers → 2019 R2)
Best regards,
Alejandro