A fix might be adding a lot more caves to the worldgen setting; or by changing kobolds to breed in a different way. Or to gen worldgens shorter than 100 years.
By default they live in fortress_detailed and also occupy cave sites which make them visible to other civs, this seems like a problem. Let me pull up the entity.txt file entry real quick for vanilla masterwork.
[FRIENDLY_COLOR:6:0:0]
DEFAULT_SITE_TYPE:CAVE
[DEFAULT_SITE_TYPE:CAVE_DETAILED]
[LIKES_SITE:CAVE]
[TOLERATES_SITE:CAVE]
Offending code here, cave start isn't in brackets either deliberately commented out or otherwise, this is unaltered copy-paste from file. In either case like conflicting [CREATURE] at the entity level it'd make them start at either per civ rather than simultaneous.
Savage races seem to be really messy with fortress starts like this, i normally play with one or two until they get annoying and turn them off, i enjoy naga's as easy early fodder though despite being unraidable in return because they are inaccessible over water until toady puts in amphibious mounts as he said he'd go towards on the FotF.
You can alter the number of caves and whether they are viewable at the start by altering the default world-generation settings to have both of these in excess on a 'create world' main menu without advanced world setting meddling. Its a field i know very little about the specifics about but changing these two variables to a default without changing anything else is pretty straightfoward as is fixing the site type.
Kobold caves are real mapped places now, so for civs and other civs who might be inclined like raptorpeople (also lay eggs) from the fortress defense mod can use them.