This was the procedure when I was working at Europadisk -
* CD-R pre-master received was placed into a CD-ROM drive and verified by customer service rep entering the order into database to have same amount of tracks and total length as indicated on provided PQ sheet, and whether it contained audio, data, or multi-session (i.e. CD Extra/Enhanced CD).
* marked top surface of CD-R master disc with CD marker with work order # (so it could be kept straight as to what is what during manufacturing process) along with internal work order forms (also indicating total tracks, total length, type of disc, amount of stampers ordered, requested turn time, etc.), and forwarded it to mastering dept. for pre-testing
* Eclipse pre-testing is run - Welcome to Eclipse Data Technologies
- where CD is read in a CD-ROM drive (usually Plextor) by Windows based workstation running Eclipse software. Test checks BLER (aka E11/E21 - C1's - the first level of error correction) C2's (E12/E22 - second level of error correction), CU's (aka E32's - which are UNcorrectable errors), as well as correctness of subcodes, TOC, index placement, timing sync, etc.
* CD-R master given a "pass", "fail" or "warning" grade. In terms of specs for this: PMCD spec allows for a BLER rate (C1 errors/sec) up to 220 - anything over would generate a "fail". A certain amount of C2's (can't remember what the threshold was - it depended on amount of burst within a single frame though) detected would generate a "fail" as well. The presence of even a single CU would generate a "fail".
* Discs with "fail" or "warning" kicked back to the customer service rep to see if the client wanted to either provide new disc - or have the pre-mastering department fix the master disc for them (by using a copying the disc's image with "secure" DAE routine, listening at any point where an uncorrectable error is noted, applying any fix of dropout or clicks at these points needed, and then re-burning a new master disc).
* Discs with "pass" grade are loaded into one of the Eclipse workstations hard drive via Plextor CD-ROM drives - using a highly "secure" Digital Audio Extraction (DAE) routine which re-reads sectors where an error flag is triggered so that any correctable errors are in fact corrected for in the copied image. These images are formated as DDP.
* DDP image is then streamed via EFM encoding to a Laser Beam Recorder which exposes what will become the "pits and lands" on a photo-sensitive glass disc. At this point (actually for about the past 20 years) all of this occurs inside a self contained machine meaning there is no need for "clean rooms" or guys in the white surgeon suits to do this anymore. Generally transfer to the LBR is done at 4x - and most LBR's are optimized for this speed (or faster) at this point - but for those who wanted to pay an upcharge a "real time mastering" transfer at 1x was offered as well.
* glass master is developed, and then plated with nickel. Nickel is pulled off, cut and sanded to size - this becomes the stamper that goes on the press.
There were lots of further quality controls at the pressing stage - but I figured I provided more detail you wanted already. Good info at Recording to CD: More than Meets the Ear
In answer to one of your questions: the replicated discs will have the pit geometry based on what is on the stamper (with potential variations due to the manufacturing process) and as such it is most likely they will trigger error flags differently from what the provided CD-R master disc did.
Hope that helps.