Yes, it's a normal Windows 10 installation.
I went ahead as you suggested and replaced texconvx64 with the official texconv (renaming it in the process), then ran TexGen through MO2. The dialog showed the background loader messages and then it successfully opened the TexGen options form (dialog box for output path, LOD options etc). I ran it from there, and it managed to complete generation. What's interesting is that I then switched the files back, and now texconvx64 also works when running TexGen from MO2. I made no other changes.
Frankly, I'm baffled as to why that did the trick, but I'm not going to complain.
Thanks so much Sheson for your help in puzzling this out.