Expanding a little on what Ken said, there is a much larger difference between DK on a PCB and DK on MAME than there is between DK on a PCB and DK on a kit-modded PCB.
MAME is emulating (that is, mimicking) the original hardware, by way of software (a driver), in order to run the game, whereas the kit is actually using the original hardware, including the original processor, in order to run the game. The kit is just a daughter card with additional code, and it bypasses the ROMs on the PCB, but it's still making use of all the rest of the RAM, sound hardware, video hardware, etc. on the main PCB, just as the normal game would.
Modding a game by way of daughter card has actually been done since the 80s. In fact, a Ms. Pac-Man PCB is really just a Pac-Man PCB with a daughter card. So Ms. Pac is technically a "Pac Man kit," and what it does is not very different than what a DK HS kit does. This precedent was set a long time ago.
Double Donkey Kong, on the other hand, is DK running on a DK Junior PCB. Hardware is close, but not identical. And I think I remember reading at some point that the timing on DDKs actually IS different - specifically you have less (or was it more?) time when the clock hits zero, among who knows how many other things. Personally I'm baffled that anyone ever wanted one of these. Yeah, you save a couple of minutes swapping PCBs, but why would you would want DK with the wrong sounds, a disfigured Junior PCB, and to pay as much or more than just buying the DK PCB straight up? The project should have been to make a PCB switcher, not a PCB mod. They never should have existed and are bad in a preservation sense, IMO.
So while there may be a good argument to disallow DDK, nobody has ever shown that DK behaves differently on one of the Brasington kits. Agree with Chris M. on the "case-by-case" thing. Since DK was untouched on the kits other than to add FREEPLAY and score-saving, and since everything else is the same in terms of hardware and software, the Brasington kits should be OK.