Hmmm. I'm not an expert on PDF, but I see what you quote as a subordinate to the earlier (in PDF/A-2) " Organizations that need to ensure that a conforming file is an accurate representation of original source material might need to impose additional requirements on the processes that generate the conforming file beyond those imposed by this part of ISO 19005."
Optimizing can be worthwhile; only you can decide (it seems to me) if lossy processes are acceptable. Lossy processes aren't limited to compression. For instance Acrobat's scanned document optimizer can perform more or less aggressive background removal. Converting to pure monochrome might be lossy, but once done, JBIG2 compression can be extremely effective.
Some more thoughts on JPEG2000.
1. It is no more lossless than JPEG in general. There is a lossless JPEG, but nobody ever uses that (not available in Acrobat, nor even PDF at all I think). There is also a lossless JPEG2000. Be sure to select "lossless" as the compression option as otherwise it won't be (if that's what you want).
2. Neither JPEG nor JPEG2000 is - to me - an obvious choice for scanned material.
3. If you aren't offered a choice of JPEG2000, but expect it, make sure you are using PDF 1.5 or later, and PDF/A-2 (since PDF/A-1 forbids PDF 1.5).
I would never consider a one way process that simply "optimized" the PDFs in any way and used only the new copies. I would always preserve the originals in case questions ever arise. Disk is cheap, even if bandwidth is expensive.
