Threads was very much a rush job (as everybody from meta will happily tell you) so i'd guess at least part of the reason is expediency - if you don't integrate

Threads was very much a rush job (as everybody from meta will happily tell you) so i'd guess at least part of the reason is expediency - if you don't integrate into instagram at all, you don't have to develop or test that integration. but threads also seems to be an attempt to dip their toes into the fediverse (whether that's well-intentioned or just an attempt to avoid EU regulators). they don't seem nearly as eager to federate instagram so keeping it out of the main app can firewall off the federation experiment.