I have used Config:IniFiles in the past and always liked the TIEHASH interface.
The mismatch in reading multi entries vs. writing that values struck me as odd, too. Though I never had the necessity to keep the syntax, as you have.
Patching: On the plus side it seems it would be enough to enhance sub OutputConfig (maybe also enhancing the constructor's config to make the behaviour adjustable).
Would have been nice if the part where the ARRAY is written, were a sub, which would offer the possibility to inhert from Config::IniFiles and override that behaviour without patching.