That might be a possibility... as long as none of the latter calls duplicates the functions of a previous one and the variable values haven't been changed by the previously called function.
Yes, that must be a prerequisite. For plugins not altering the database this should be OK as long as the code uses alters only local variables. For plugins manipulating the database one need more caution, and you will probably as a minimum need to order the plugins in the right order, or even remove the routine in question.
However, if I should rewrite my own 'handleCustomFunction', I guess I need to make a loop in there and I will possibly need to undef the first routine, before performing require on the next with the same name of the next plugin? Am I right? I am not into all details of perl, but I guess 'undef' is the right keyword? (As far as I can see from perldoc...)