The main problem with the eMMC is if you are writing to it all the time, like an SD card it will fail in the end but unlike an SD card it is not easily replaceable.
The ideal solution would probably be to have the eMMC set up as a read only boot with temp files and any other writable paths either on a ram disk or SD card or combination.
Or you could just not worry about it and when the eMMC fails start using a SD disk!