We have two plants about 2 minutes apart. We tried for a bit to go multi-plant on those two, but in the end when we switched over to single plant, multiple warehouses, everything got much simpler. Yes, there were issues with "Purchasing issues (deliver to addresses), accting issues, maintenance issues, scheduling issues" when we switched to single plant per city, but those were all relatively easy to overcome (though I admit, all of macro and micro scheduling is done pretty much entirely outside Epicor, and we haven't started using PM module... yet).
The unique resources / warehouse names is actually a blessing in disguise. We established a common prefix for all of our product groups, resources, warehouses, etc.(e.g. everything over here starts with LM- and everything over there starts with LW-), and it becomes pretty easy then to distinguish between the two "plants" that are actually one plant. Sometimes I forget that we do only have one plant for these two facilities. Another point I'd make - a lot of the struggles at go live were overcome by changing our business to operate in a manner that worked better with Epicor. If management pushes back, just re-quote your Epicor consultants: "You don't want to spend upwards of one million dollars just to end up with the exact same system and processes you had before."