There are quite a few nuances that are used to tell a 39 - 42 Mercury engine from a Ford. Also, there are WWII engines that are 239 cubic inches and closely match the 41-42 Mercury engines.
I won't try to get into all the differences - plenty of sites have shown the blocks, the raised intakes, the coolant holes, the 'pencil test', etc..
For many flathead performance nuts, the 99A Mercury block is special . . . even though it really makes little sense to believe it is any better than a good 59AB 239 block. I have a 41-42 style Merc style engine in my 32 Cabriolet - it was an engine built for WWII military applications (dual-sheeve pullies, special oiling system mods, etc).