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As config.pro files (other than config.win) are pure text files, You can use a simple OS script to concatenate multiple files, e.g. one general, then a project-specifc, finally a user file. If the same setting is defined multiple times, the last one wins.
You can even generate additional entries in this script.
If You remove any config.pro files from the standard folders (ProE install, working directory, home directory - wherever this in in Windows), You can place the resulting file in the working directory before ProE is launched there.
Create a new ProE start script, which creates the config.pro and then calls ProE.
We had that working even in a mixed OS environment (Windows and UNIX) using a single Tcl script and a single set of source configs for all.