I have another DIY ECU, but I made it with a side mount internal adaptor PCB like the one above. I can run factory ECU plug, screw, etc, and probably even the MS Ampseal, without touching the ECU. It's just too versatile and compact to not be the best choice, and can make any unit PnP easily. You can even use the adaptor to directly solder wires to an single external connector that plugs to the OEM loom. Connector to connector, is easier and cheaper than connector to connector to wire to connector to connector.
Now the problems. Mine is a single row THT 90º header, and that makes it rather delicate so you have to plug in carefully. It gets bolted together after connection, so it ends up strong, but any lateral force bends/flexes it up. The other problem, like the pic above, is that there is wasted space in the butt connection. If I was doing it again I would use a std vertical header and and flip the adaptor PCB. This would cut length with the overlap, and still keep the height down. Hell you could put the header in the middle of the ECU PCB and have most of it overlapping, except for the actual plug, to make it even shorter.
I did buy a JAMA edge connector out of an arcade machine, but that has the extra length and extra height problem.