I think the flawed assumption here is that the potential advantage of having a connector (or anything really) fit a .1" perfboard outweight all the other advantages of not having it fit - like how easy it is to route on an actual pcb, strength, density, etc.
Also, most manufacturers no longer live in a imperial-driven world. The only things really still imperial (but actually it's not) is SMD footprints like the typical "1206, 0805, 0603, 0402" (even though I believe they are actually defined in metric and then translated to imperial to match, with a 0402 actually being 1.000mm long and 0.500mm wide). In fact, I usually get annoyed by the old DIP footprints and headers not fitting nicely on my metric grid PCBs, making nice allignment a PITA.