You don't have to copy it when upgrading.
With TDMD.INI in the LOCALAPPDATA\JPSoft directory you don't have to copy because it is shared by all versions, which brings us back to the topic of the OP, namely that shared configurations lead to conflicts in directives and configuration files under %ProgramData\TCMD<nn> must be copied.
In other words, if you never need to have multiple versions side-by-side (except the one version you're upgrading to) then your best choice is LOCALAPPDATA, if you do want to test backward compatibility of your products, do ProgramData.
Can the installer copy the inifile for you? Always? No. The installer cannot know which inifile you are using since multiple files with a non-default name in a non-default location are allowed and you probably have them in a hyperlink, somewhere. Who knows?
Well, you do. You know in which way your setup is non-standard. So, you can script the hell out of this! Put a folder MONITOR on %ProgramData\JP Software\ ! ... and let us know how you fared.