Years ago, CSX eliminated almost all their grade crossings. Part of why you never hear about Tri-Rail having trespassing accidents. Don't know who paid for the upgrades. Granted, CSX (and their predecessors) is MUCH larger than FEC. So, would BRIGHTLINE be spending the money to upgrade FEC's ROW? Cities? How would they separate grade?
I know of a private passenger line in Tokyo put their entire train line underground over the period of like 5 years. It was an amazing feat! Other lines have been completely elevated - all without significant service disruptions. Obviously, the FEC can't go underground, but can it - in any economical universe - be raised in the most densely populated areas?