i think flash process is not compatible with standard cmos - many cmos processes cannot make the thin tunnel oxide and the normal mosfet oxide. also the flash floating gate is not really easy to fabricate with standard poly gate processes.
that's not to say that a guy with a good cmos process can't make flash, but it uses some special processing that most of the MOSIS guys don't do.
also, since programming voltage is about 12-14v, this is above the breakdown voltage of many small cmos processes (around 4-8v). you need HV mosfets as well as the tunnel oxides and floating gates. THEN you can make flash.
TSMC sells a block of flash to drop into your asic design, I think around $30K to license this. The flash is very good quality and easy to use - originated by SST (silicon storage). I think it uses a split-floating gate. Only if floating gate is charged (programmed) and normal gate is on does the cell flow current. Very reliable, but individual will have a hard time to pay this licensing fee. But hey, a single process run of 24 wafers is around $65k from them (If I remember correctly), so maybe if you have good funding this does not sound like a lot of money.. to me, it's WAY too much! I mgiht use external program memory, and build my micro on a cheap 0.5um process.