It must be a brand thing. I use almost exclusively Gigabyte boards and none of those, at least up to now, have it. Hopefully Gigabyte and all the others will follow suit. But don't know what you mean by "have to run without a case if they were without". For years we all just used a flat tip screwdrivers which still works just fine - or one of those button switches I linked to above. No big deal.
I guess we can thank the continuous miniaturization of components, As motherboard dimensions remain the same, motherboard makers are able to squeeze more and more features in the same real estate.