Fortunately we do not actually import any specific certificates, so my solution is my simple script (in my post from May 3rd above) that just moves the old version's .acrodata files so they don't even try to get imported.. I could not get it to run as part of the "Other Programs" part of the Wizard, be we use a Kace 1000 appliance for management, so I simply made a script to run that before installing the program. It's not a very clean workaround, but it works for what I need.
There seems to be no options in the wizard to do what we need, and I tested (as listed above) a lot of registry keys and other fixes with no improvement. The only option seems to be to move or delete the .acrodata files to prevent the popup asking to import certificates, or to live with the popup. I hope someone proves me wrong.