this is pretty clever. if you keep things square, with fixed girder lengths in multiples of unit length, and unit length being the size of your typical hub (the distance between 2 adjacent dock points of your basic 6-way hub). modules could be designed with linkups that match girder length+2 (for hubs and t-pieces). to expand beyond square is where things get tricky.
say you want a cross-ways girder as part of a square frame and say 1 unit = 10 meters and distance between the center of the hubs is 100m x 100m (or 10 units). provided there is space for an angular dockpoint (say one of the orthagonal docs rotated 45 degrees about the intersecting axis) that doesnt clip with the other docks. the distance between the dock center and the dock is 0.5units, and in this case it would be about 5 meters with a 90 meter (or 9 units) girder (the whole frame would actually be 110x110m, given the extra 0.5units). the distance between kitty corner hub centers would be sqrt(10x10+10x10) or 14.14214 units -0.5-0.5 for the distance between the dock and the hub center. so this would require a girder 13.14214 units long. what you could do is add the extra 0.14214 to the hubs instead so you can have an integer-length girder. you would only need to extrude the dock face of the diagonals by 0.14214*0.5 units.
getting even more 3dimensional, say you have a cube built with 2 of those frames connected by 9-unit girders (gonna use cell units from here out). now the distance between top right hub on the back frame and the bottom left hub on the back frame is sqrt(10*10+10*10+10*10), or 17.32052 units. we can do the same thing as last time and take up the excess 0.32052 space at the hub and use a 17 unit girder. at this point we kinda hit a problem though. say we want to use 5-unit girders, now the distance between the same 2 modules is sqrt(5*5+5*5+5*5) or 8.66025, and if you wanted to use a 7 unit girder you now need to take up 0.66025*0.5 (beyond the 0.5 needed) at the hub.
essentially what your creating is a virtual lego set. if you have used lego for as long as i have you grow to respect the engineering behind the system. my point is that this is something that would require more engineering that graphics design. if you come up with a decent set of design rules then you need not model the whole thing yourself. if you make the standards for the system up front and well documented, providing guidelines to follow for people wanting to create new parts that mesh well with the existing system, then you would have a very powerful way to build whatever kind of installation you want with with only a small library of parts.