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Sorry no idea what CloneCD does, but maybe.
However with CDs you have one generic format (aside from cd+g etc) and variants of that format and its encoding can be used to protect a cd.
On (original) Amiga games there are hundreds of formats being used. You must know what you are reading in order to verify that what you read does not have errors. That's why analysation is needed. Each format is described with a script/descriptor, that the analyser tries to match against the track format, then picks the best match. Obviously these scripts contain information on how to verify the data, calculate different checksums etc. Once the format is found the relevant data is abstracted into the "language" used in ipf files, and produces the ipf file.
It's pretty much described on our older wip pages.
Original duplication worked the very same: they had a master disk read according to the trace script (similar to our scripts), then the data was written to disk according to the instructions contained in the scripts.
While real duplication generated the data directly onto the disks, ipf preservation stores the data needed for magnetic recording/emulation in the ipf file. That means the data stored is not "raw" data: that is generated on the fly by the decoder library.
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