no, they weren’t at all clear how they would apply and to whom. you think you know, because you choose to believe what you wish to believe.
all means all. it does not say “federal prosecutions” it says “all prosecutions”. the idea that double jeopardy does not attach to the states is just plain ignorant since the only prosecutions at the time of ratification were state prosecutions. why would they create an amendment to restrict a power they didn’t even think the federal government had?
where in the constitution is the federal government empowered to criminalize behaviors the states already had the power to criminalize? these are the police powers, and they are reserved to the states. what possible capitol offences did they envision other than the ones they exempted under was powers? was the federal government going to make murder a crime federally? robbery? were they going to make violating the commerce clause a capitol offense?
federalism does not mean the states can ignore constitutional prohibitions.