You're talking about a $40 tool just to flash the storage vs a part (micro SD adapter) that they give you with the SD card for free because it's so cheap.
Also doing a quick survey for the rated cycle counts on M.2 vs SD card slots:
M.2: I found this one [1] which is $0.768 for only 60 cycles
SD: This one [2] is $0.6256 for 5,000 cycles
I'm not sure why you'd say M.2 is more reliable, considering users often cycle storage dozens if not hundreds of times.