This is what I was going to mention. Though Not a cop myself, My Mother, 4 Cousins and 2 Uncles are, and in the past they told me that vehicles entering the state that are registered out of state can be non compliant with the local state laws provided they are "Passing Through". If they are owned by a resident of the state by registered out of state then they are in violation if they have been in the state for more than one month unless the owner can show that they are a legal resident of the other state. Student Status can modify this status as Students are not required to register in the state of their school (if out of state) provided their "legal" address is still their parent's house.
All of that stated, an officer can pull over any vehicle he wants, and in the above cases only a warning is typically issued at the most. If a vehicle is BLATANTLY illegal, and or dangerous (unsafe), they can require that they take the offending vehicle out of the state immedialy, or else tow the vehicle to their destination.
At least that is how my state works (Mass). Also there are non visable violations that can also be found. for example, In New Hampshire they do not require car instuance, and MA has it mandatory. If you drive an Uninsured vehicle into MA you may not get a ticket immediately, however if you get into an accident, or commit another violation that causes you to be pulled over and found not to have insturance, they will tow your vehicle and you will not get it back until it has insurance, even if it is not a violation in NH, MA will hold the car for Insurance.
All in all, before people get upset, Alll of this is fully specualtion, If you get a dickhead officer, he may try to screw you and could get away with it. Every state has diferent relationships with the states surrounding them and how the relationship has been could reflect greatly on your personal situation.
If you know your in violation of the local laws, make sure your not doing anything that would make you a target (stay under the speed limit, no road rage, etc) and if you are not blatently violating local laws (say a 10 inch body lift, 50 inch tires on a JK 2door etc) then you should be ok.
If you are pulled over, don't be an asswhole, doing so makes the officer an exponentially larger asswhole, and trust me you don't want to trigger asswhole mode in a police officer. Explain any lift, mods you may have with the officer. Do what I do on my lowered/modified car and get all the applicable laws together on a document and laminate it, put it your vehicle and put all of the calculations that show that your vehicle is leagle in your state to help the officer know that your consious of the laws in your own state, and that you are only driving through. If you are not a dick you will probably get a "Ok, just keep it under the speed limit and be safe" and be on your way..