but it's likely because they just completely destroy any kind of out of order execution.The same goes for the longer sequence of individual pushes or pops --- they all depend on the stack pointer. In fact, the single instruction needs to only adjust it once by the total number of registers pushed/popped (since it is a constant).
In other words, PUSHA/POPA already decode internally to a bunch of moves and one ALU op for the stack pointer which can be scheduled OoO. All they needed to do for 64-bit mode was adjust the constant (by multiplying it by two) and emit more uops for the additional registers, but they didn't for some otherwise inexplicable reason. All the machinery to do it was existing.
And then there's the fact that modern compilers are likely already avoiding those instructions because of the timing of saving extra registers that you aren't using in a given function, it probably just doesn't make much sense to keep them anymore.
Compilers won't ever use PUSHA/POPA but lots of other code will --- BIOS, executable packers, OS state-saving code (the perfect example of what these instructions were for?), etc.
See the story of SAHF/LAHF for a similar and even more astoundingly bad decision.