ITAR is a good reason to keep them apart for now. Do to SpaceX making rockets, they can only hire US citizens and a bunch of other annoying requirements by ITAR are needed to be met.

Its easier to keep the companies separate just from a compliance standpoint as what would otherwise be a minor issue can turn into a hundred million dollar fine (eg: someone accidentally given access to the wrong file server). If everyone in your company is a US citizen its much harder to accidentally create an issue under the eyes of ITAR.