There is a difference between core and CPM - core can not create adjacent ("Back-to-back") burst accesses to memory, because of peculiarity of core load/store unit. The CPM is optimized to use memory more intensively, and can issue memory accesses without any gap. So, if some "overlap" problem happens on adjacent memory accesses, where previous memory access somehow interferes with next immediately following memory access, than this problem may happen on CPM-initiated memory transactions, a will not happen on core-initiated ones.
The same very highly optimized intensively memory usage algorithm is implemented in DMA engine, so you can use DMA to test this problem.
To answer your questions:
1. There is nothing re-programmable inside the processor. Internal microcode ROM is one-time programmable at factory and can not be updated. You can only have "microcode patches" applied to this ROM to fix a particular bug. All known bugs are listed in device errata:
https://www.nxp.com/docs/en/errata/MPC8280CE.pdf
2. SDMA channel usually works perfect and does not require any debugging. There is not too much information in SDMA-related registers (MPC8280 Reference Manual, Section 19.2), only transfer error bit and related MSNUM number. You can also have some debugging information in FCC-related memory structures, but I do not think it will be helpful in this case, because FCC does not indicate any error in this case, as far as I can understand from the description.
3. To make sure CPM read transactions are good, you can use the same SDMA functionality to transfer data from memory to memory, as common DMA engine. Please look MPC8280 Reference Manual, Section 19.3
https://www.nxp.com/docs/en/reference-manual/MPC8280RM.pdf