did not intend to limit offenses only to those in existence in 1789. Congress could, apparently, define new offenses if they arose in customary law."
and
"It would be a mistake to infer too much about the framers' and ratifiers' conception of the offenses clause from these historic excerpts. The framers understood that certain acts violated the law of nations; they were aware that the states had failed to deal adequately with those acts as crimes under their common law and that the law of nations was imprecise'-the new nation needed both a way to treat such offenses and uniformity."
https://scholarship.law.vanderbilt.edu/cgi/viewcontent.cgi?article=2133&context=vjtl
The context is very clear - congress had the ability to define and punish offenses against the law of nations
Sure, debate and ratification MAY have been about certain offenses of the day, but they intentionally DID NOT limit the clause to those offenses - they wanted congress to have the ability to deal with other well defined defined law of nations issues. And immigration control is and has been a well defined law of nation issue for centuries.