I don't see any reason why it wouldn't work. If you take a big building like the Embassy or Prison addons, you can see that while they are big, OFP has no trouble working out where the walls are. And if you were to take them apart they would probabaly work fine.
It could be that the "blocks" are too big, try making them smaller (not in scale size, but less components in a block).
Also, geo lod's should be bigger than the walls themselves.
Its probably not this, but: Binarize isn't the most reliable of utilities, I have found. But even that shouldn't mess up the walls having no depth etc.
edit
One thing you might want to remember is that, in O2, where the two red lines cross is the centre of any .p3d. There's some relevance there, I know it :hmm: