The first faulty scenario can be solved by placing library modules in a subdirectory structure so that they have different path prefixes. The new filesystem layout will be:

projectA/ProjectA/MyConfig.pm
projectA/run.pl
projectB/ProjectB/MyConfig.pm
projectB/run.pl

The run.pl scripts will need to be modified accordingly:

use ProjectA::MyConfig;

and:

use ProjectB::MyConfig;

However, if later on we want to add a new script to either of these projects, we will hit the problem described by the second problematic scenario, so this is only half a solution.