Affinity Designer is working. The mistake I made was that I assumed you all were using Affinity Photo. That was where I was having layer issues.
Photopea is free, and the layers work - but it's an online editor - CTA3 can't send files to it.
Thanks especially to Vepop for having the patience to help me figure that out (on the FB CTA3 pages).
So to conclude, the 2 Photoshop alternatives that have worked (with CTA3) for me so far are Krita (free) and Affinity Designer $49. I am going to go with Affinity Designer because it's interface is awesome and it also has the vector tools, plus photo tools.
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