Just to confirm, the workflow you are envisioning is this: you run polyspace-configure on your build command and share the generated Polyspace options file with others. They will then run polyspace-bug-finder or polyspace-code-prover using your Polyspace options file. You are running into the problem that the -sources lines in the options file uses absolute paths to source files.
You can write a simple search-and-replace script that takes the path to your root directory and replaces it with another root directory. Users who receive your Polyspace options file can run the script to replace the root and create a modified options file (or the script can be made to run automatically on certain triggers such as checking out from an SCM tool).
Just to let you know, the intended usage is: polyspace-configure and polyspace-bug-finder or polyspace-code-prover are meant to be run as a pair by every end user. So like this:
polyspace-configure -output-options-file options.txt buildCommand
polyspace-bug-finder -options-file options.txt
The reason is, the end users might be adding new source files which would not be captured by an options file that was created earlier and shared.
Of course, I understand that adding new source files is not a frequent event, and you probably have other ways to keep the Polyspace options file updated for new source file addition. In that case, a search-and-replace script like the above would be the best way to go.