The PCB construction is curious (which you say is multi-layer) - why use a grid of 0.1" holes? Is that so it could be easily jumpered? Can you tell if the traces run through the holes or between them?
I don't have the patience to reverse-engineer these types of boards, but I do find them really interesting to think about. CAD was just getting started (I just looked up that Gerber format was released in 1980) so I wonder if the masks were hand-drawn.
The grid is 0.1" holes because that's the spacing of most components; it's a bit like perfboard. If you're asking why they used a grid instead of a normal-style PCB, I'm not sure. It probably makes manufacturing the boards much easier since you can drill the holes with an assembly line rather than one at a time. The traces go between the holes; the traces are very narrow, so two traces can fit between a pair of holes. That's probably the tradeoff, that your traces need to be very precise and you probably need more layers because of all the holes in the way. The layout was probably done with CAD; PCBs with CAD go way back. IBM was doing circuit boards with CAD back in the early 1960s, using a flying spot of light to draw out the PCBs on photoresist.
When you say that the 125 added memory management, what does that mean a little more specifically? My guess is either PDP-11/z280 style paging without page tables (the 16 bit address space makes just having enough IO registers to cover the address space tractable) or some simple segmentation hardware, but it'd be neat if there was another hardware object capability system I didn't know about.
The Mitra 125 had memory segmentation. It seems similar to the 8086, with descriptors that specified base address and length for a segment. Accessing memory outside a segment caused a trap.
I don't have the patience to reverse-engineer these types of boards, but I do find them really interesting to think about. CAD was just getting started (I just looked up that Gerber format was released in 1980) so I wonder if the masks were hand-drawn.