I have seen these branding mismatches before (first remarking on a midget set that Gordon on the G owns with a PLOMB box and PLVMB tools in it), but I agree, Don, it does look like it's more common (or at least less unusual) than I originally thought. And your unmolested Challenger 5200Y set is a great benchmark for the case, since we know for sure it isn't any older than 1939.
As I surmised briefly above, I imagine they had them stacked up somewhere and they just drew from that stockpile when they were putting sets together. And it seems evident that their production of (or order for) chests and boxes exceeded the number of sets they were selling. At some point in the late 30's and into the 40's, they were filling the boxes with tools and sticking decals on the lids that were much newer than the boxes. So it must've been quite a big stockpile!
(EDIT: This is tangential, for WWII guys, but it may also help date the sets in PLVMB TVVL CV LVS ANGELES boxes to mid to late war, and the sets in PLOMB TOOL CO LOS ANGELES boxes to early war. Since the directive in the factory probably would've been to use up the old boxes first until the stock was depleted.)