Of course DoM (that supports ATA-2) is a very convenient solution if data exchange is less of a requirement, but I don't concur with the above since CompactFlash IDE mode is a full T13 compliant implementation, albeit with CMOS levels as mentioned. Conversely DoM are typically TTL (
eg this) and sometimes implement SMART.
As mentioned already, many of the IDE-to-CF adapters are the source of compatibility issues (perhaps 90%), the remainder being occasionally we come across CF cards that don't correctly implement 8-bit mode. The issue with the adapters is that the 5V power is delivered through a diode, actually at about 4.3V - which is totally out of spec for either 3V3 or 5V operation. Cards from all the common brands - SanDisk, Transcend, Hitachi, PQI and Kingston to name just a few - have been pattern tested for hundreds of hours on these adapters.