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I don't understand why they populate MiniPCIe vs an M.2 slot.

Anyone know?

Only thing I can imagine is the key variants for M.2 are more complicated.

Compatibility? Something like Iridium radio might still be using miniPCIe. And you wouldn’t want adapters in embedded.

MiniPCIe allows for adding wifi, network, storage (M.2) and other cards.

M.2 limit to only storage.

M.2 can be used for PCIe (including NVMe, wifi+bt, LTE modems, etc), SATA (storage only), or other weird stuff depending on the keying.

Afaik large share of embedded WiFi/BT and 3G/4G chips are USB ones?

m.2 can have USB lanes aswell

Aren't there WiFi and Bluetooth cards using the M.2 interface?

Yes. The A/E keys allow for PCIe and USB, among others. My Intel Wireless-AC 8265 WiFi+Bluetooth card is an M.2 22x30 card.