Exactly. And this is also the thing that should be the most future-proof, because IIRC it's not on the CPU board (which is in principle upgradeable) but it's on the main PCB. If a next-edition Pyra would have an upgraded CPU board (perhaps even an x86 based one with a full OpenGL GPU?), then it would make sense, and it would be possible, to give it more RAM as well to match that. But the internal storage on the eMMC is still going to be what it is.
I immediately want to add though that it's not that important to have a future-proof eMMC, since there's still the µSD slot that can override the eMMC, and also, I imagine that the idea of the "upgradeable CPU board" is mostly something to simplify the design of potential Pyra successors, but it's not really meant to actually upgrade Pyra 1 units to Pyra 2 units: the Pyra 2 would probably still have a slightly updated main PCB as well, with perhaps a faster/better wifi/4G chip, faster SD card slots, and a new eMMC. At least that's my prediction.