I think the main problem is reliability:
- the mechanical contacts are not as reliable as soldering
- I have read here many people complaining about faulty, slow or just incompatible SD-cards, but I can't remember anyone complaining about faulty internal flash
I personally did got problems with a (Micro)SD Slot - and this one will not be changed/switched very often.
I read many onboard flash problems, but with the Seagate Dockstar.
There is a special programm needed to go around the errors in the flash chip which has "bad sectors"/cells