The body mount nut plates are designed to "float".
They are held in their approximate position with a sheet metal cage.
They need to float and not be welded into place so they can align when installing the body bolts. (They frame to body alignment is not exact)
Yes - it can be tedious getting the bolts started.
I usually run a tap thru the nut plates to remove excess rust, etc and then grease them.
I also run the bolt threads across a wire wheel and give them a coating of grease before starting them.
Sometimes it helps to start a longer bolt a couple of threads, back it out leaving the nut plate in the correct position. Then gently insert the body bolt without disturbing the position of the nut plate.