Remember that there are parts on the bottom of the PCB, the EMX is flat, so the USB stick will not mount as easily.
I still stand by "solder a micro SD card onto the PCB. It is flat on the bottom and it is a PCB, like the EMX. I just don’t know what will happen with the plastic top casting…
If someone else will looking for something similar Im find one product:
Cactus SDChip:
Card Capacities 128MB to 8GB
Supports CPRM
Supports SPI Mode
Voltage Range: 2.7V – 3.6V
Unique Electronic Serial Card ID
Sustained Reads up to 22MB/sec
Sustained Writes up to 16MB/sec
BGA 
Yes but for production devices I think this will not be big problem. For developing need’s they offer “SDChip™ Adapter” which have already soldered SDChip… Adapter have one side flat so can be “embedded” into PCB but is little bigger than normal SD card(49x43mm)… More info about adapter is in Product Manual on page 23(Appendix B.SDChip™ Adapter).