I just did a couple tests. I uninstalled Paint.net completely between each test. 4.2.8 always launches fine no matter which method of installing. These tests were all manually just double clicking the msi or exe, no extra parameters.
If I install 4.2.8 with the executable, then install 4.2.9 with the executable, everything works fine.
If I Install 4.2.8 with the msi extracted with /createmsi, then install 4.2.9 manually with the executable, I get the error.
If I install 4.2.8 with the exe, then install 4.2.9 with the msi extracted with /createmsi, I get the error.
If it's helpful, I'm attaching my msi output log
output.log