Leaks were allowed in the bsp.exe, However vis testing didn't allow them though (always hated this part, took forever)
i musta been thinking about quake2. quake1 map compilation was less strict. you could compile lighting before compiling vis in quake 1, and if you were using one of the more modernized quake engines, like darkplaces for example, you could get by without the viz and would allow for some transparency to be implemented. q2 maps on the otherhand required a vis before you could even think about lighting. with a huge folder full of unfinished quake 1 and 2 maps, many of which just wouldnt compile, im pretty sure that freespace would just break if we tried to implement that kind of geometry abstraction system.
Also it would be very nice if modelers would use single submodel to represent the main hull of the ship. Certain things in the code (namely modeloctant stuff) assume that primary 'root' submodel is the main hull and some fragment of the main hull. This will lead to 'interesting' effects when ai tries to find target spots on the hull against which to attack.
i sometimes did this in truespace. my original version of the chaos for example, was modeled and uv mapped in ts3.2 and was made up of primitives (go figure i was using techniques i learned in quake mapping). converting the model was a nightmare, considering the tools we had back then really sucked. my solution to this problem was to
pirate aquire ts 4, which had per-face uv mapping. it was hard to make work but it allowed many solid mesh models to be created (these are the classic models, many of which have since been htled). this is why my early models were very stable (also since i didnt export to other proggies for uv editing). now that i use max, i really like the attach feature. even if you dont seal stuff, you can use this to make a bunch of object one object.
Really though there are much worse geometric boogiemen than unsealed meshes. 
like micropolies, bad normals, no normals, duplicate polygons and so on.