Several connected webpages and documents starting here on the On30 Coalition Module St@nd@rds (OCMODS)
I don't want to duplicate what Bob has written on Railway Bob's Module Building Tips except to add a bit to his T-Nuts For Alignment Pins/Bolts
Using blind T-nuts to help align Module Interface Plates is a great idea.
From experience, it can be a PITA to get the bolts to start threading into nuts. Cross threading is a real hobgoblin. So, I suggest using longer bolts with the threads filed off the first 3/4" of the end. Then you can slip the bolt into the nut nice and straight and then start turning without having any crossed threads.
This will give you alignment AND make it easy to thread the nuts and bolts together...
Use an even longer bolt and you can add a wingnut for easy finger tightening...
Having the Blind T-nuts on one end of the module and the "sighted" T-nuts on the other will work for N-Track style modules with a front and rear.
For Free-Mo style modules that can be turned end-for-end you have to put a Blind and Sighted T-nut at each Interface Plate as shown in the diagram.