Updated the BIOS, resetted BMC, reseated CPU, pulled the battery, waited, put it back, eve, kicked the tires... still no luck. Adding second 48 Gb Kingston ECC UDIMM makes it unbootable. Contacted Supermicro support, they also told about the firmware, then mentioned that Kingston is not on their QVL, and ended up with "you may need to RMA the motherboard and memory to us, so we can debug". Since I'm not in a big rush, I might just do that, and see what they come up with. Haven't decided yet what I do in the meantime.
Interesting that I can run a single 48 GB module at 5600 MT/s. I wonder if that's the problem, and if yes, is there any way to tell the motherboard try a lower frequency when there are two DIMMs. Can't find any BIOS settings for that though.
Fun fact, 48 Gb ECC in DIMM A1 and 16 GB non-ECC in DIMM B1 also work together fine (64 Gb total, work in non-ECC mode).