I don't really understand the question: there are legal differences between (a) entry into the US and (b) travel within the US. The federal government has asserted that there are carve-outs to the Fourth Amendment for the former (the "100 mile" zone), but that's definitely not the case for the latter.
As a citizen, it makes little difference. If I want my rights respected I better not leave the country? That makes no sense. I see no reason why CBPs immigration duties can be used to bypass 4th amendment but TSA's duty to regulate interstate commerce as outlined in the constitution can't use the same logic by saying regulation of commerce to acheive safety of travellers and those in the ground supersedes the 4th amendment because unlike international travel where you can only go to canada and mexico over land, interstate travel is possible to most states without flying.
