IF the failure rate of eMMC is very low, it might not be worth worrying about. Which is why I would like to know the failure rate.
It's still worth worrying about if you care about device longevity.
And even not considering that, microSD gives you the advantage to increase your OS storage size, easily move your OS into a new Pyra, (if your Pyra dies for some other reason, for example) or a way to easily switch your base OS on your device. (have multiple micro SDs for debian, arch, android, etc.) Not to mention, instead of having to spend time flashing the device before shipping, EvilDragon can have a premade image that he copies onto his microSDs that he just inserts into the device as soon as he gets it and ships it out.
-God Ginrai