Yeah, there's just not enough physical space for more than 1 M.2 drive and 1 PCIe x16 slot on mITX.
Even B550 is overkill, really since it has more PCIe 3.0 lanes than any of the other onboard parts could possibly make use of.
Potentially if you were hoping for 10x 10GB/s USB3.2 ports you'd be disappointed with B550 which tops out at 6x 10GB/s, 2x 5GB/s, and the rest at boring 3.1 speeds - but 8 fast USB ports is proably fine because that'll cover the rear IO shield nicely and if you get more than a single internal USB3.2 header on the board then something else important has been sacrificed to make room for it!
Even squeezing a single M.2 onto an mITX board is a challenge - the two options are a riser card
above the B550 chipset itself, and usually the CMOS battery, audio capacitors, and audio/ethernet hardware, or secondly in that same location but on the reverse side of the board. I don't think you could have an M.2 in both locations as the traces for both are in the same space whether the M.2 slot is on the front or back of the board - you'd need a comically-expensive 16-layer PCB or something to make
that work
@TheLostSwede has confirmed it's a typo in the manual so, nothing to worry about, but I was referring to this typo (cropped to slots 2, 3, and 4, since slot 1 is obviously hanging off the CPU):
View attachment 204469