Interesting idea, but personally I would find it unsuitable because I think it is micro-managing prototyping too much..
This prototyping micromanagement is backwards compatible and will not deviate into proprietary solutions.
The rules should not be viewed as dogma, but only as guidelines for action.
The repository has even got detail down to placement of text, and prescribed connectors. The grid may be important for things that need more precise alignment (such as mating connectors, or assembling mechanisms, or optical work) but your design is using jumper wires, which do not need the boards aligned.
The connectors are arranged in a grid for butt-joining when a regular jumper is used instead of a wire jumper, like on motherboards. This saves space and the number of protruding wires.
https://mpp2508.github.io/docs/03asmb/unsorted/img/010.pngThis photo shows how the logic analyzer module is connected to the USB-B module (below, purple and green module).
Look at other photos and you will find such connections.
The defined 5.08 mm spacing and 2 mm hole diameter feels impractical,
Using breadboards for soldering as a blank for modules when there is no point or possibility to make a printed circuit board.
And these breadboards have a pitch of 5,08/2. If you use a different pitch on the base, this will be difficult. Butt jointing will become more difficult.
https://mpp2508.github.io/docs/00blog/00prehistory/img/009.pnghttps://mpp2508.github.io/docs/00blog/00prehistory/img/010.pngAs for the 2mm hole, m2.5 and m3 would be too big for a 5.08 pitch. Maybe m2.5 would have been suitable, but I decided on compactness and butt jointing.
since many off-the-shelf existing boards may not fit.
Adapters are provided for all kinds of different modules.
https://mpp2508.github.io/docs/02m/adap/mpp_a_01/img/001.pngThere's an Adafruit product which tries to address that, by having slots. I think at least making your base board have slots, or at least some slots, may improve it.
I haven't seen that from them. We still need to start collecting similar concepts over the network.
Well, as was said above, the problem of third-party modules is solved by adapters.
Personally I prefer to use a piece of plastic or wood, with holes drilled for board standoffs or spacers. That way works with almost all existing prototyping and breakout boards, using (usually) standard M3 screws. It works for plastic (often transparent or translucent) covers too.
I tend to keep a small amount of opaque, clear and translucent plastic sheets, 3 mm thick, and drill some holes in them, to act as a base and/or cover. The end result is as robust as drilled plastic is, and can look as neat as a regular-arranged grid if drilled accurately.
Well, it's hard to switch from familiar solutions because it's a habit. And you also need to make an effort. As our system administrators say, if it works, don't touch it. But on the other hand, you've probably had cases when you reluctantly mastered something new, and then thought about why you didn't do it earlier. Maybe the same will happen with mpp2508, who knows.
But I appreciate not everyone might feel comfortable cutting/drilling plastic (although there are services for it, but chargeable).
There is such a thing. There is always a task of balance based on personal capabilities.