Are PC Engine CDs completely non-standard/out of spec, or are they simply an antiquated or out of date standard?
Possibly, it's an out-of-date standard, although from my researches, they meet the iso standards (at least, ecma-119, as of sept 1998).
The real problem, however, is the same one that prevents you from playing turbo cds in a pc cd player: Micro$oft decided that data cds must have the data track as track 1 on a cd. Note that that is -not- in the standard. It's something imposed by micro$oft in their cd drivers, and adopted as a de-facto standard for cds.
The net result of this is that most places refuse to burn a cd-rom where the data track is not track 1, even though they may be iso compliant. The drivers on the pc's they use to run the pressing machines just cannot handle those cd's.
The data track is not ISO-9660 compliant... that is likely the issue
No. The issue, if there actually is one, is that a data track requires specific length gaps before and after it. It -may- also be a requirement the the audio tracks be seperated by 2 sec gaps, though I have not been able to verify that. Normal cds do -not- have this requirement, so I can't see why a data cd would. But it might be a problem.
With that said, there should be no reason they can't make a bit-for-bit copy of the master. If the cd-r master boots on a turbo/duo, a bit-for-bit copy should boot.
However, it appears they can't/won't make a bit-for-bit copy for some unknown reason.