No one mentioned the obvious: if a small monster is living in a lair convenient for much larger creatures, the original builders were of a larger size, and the kobolds either dispossessed them or (more likely) moved in after they left for whatever reason. Not very clever creatures can recognize the utility of good stonework especially when they lack the cleverness to build the like. Then, breaking it down to kobold-sized spaces is hard to do in a permanent and large scale manner. Wood can burn. Earth can be washed away with a good spell. Etc.
Kobolds that can't find vacant buildings would build to kobold scale, but those would be lacking in other things. Though a party reduced to crawling through tunnels would probably not find those lacks advantages.