The NEC profits--which are expected to amount to around $400 million per year--could pay for debt service on these loans, and plus, interest rates are extremely low and have been extremely low for the last few years...
You keep harping on the possibilities of Amtrak obtaining RIFF or other low interest federal loans to pay for NEC infrastructure projects. The problem is that, unlike a state or city government when it issues 20 or 30 year bonds to pay for road or transit projects, Amtrak does not have the power to levy gas, sales, or real estate taxes that governments often rely on to pay off the bonds. OK, maybe Amtrak could levy a surcharge of some sort on passengers or on the commuter railroads, but it would make Amtrak less competitive and make for a even more complicated financial relationship with the all commuter agencies.
I expect that the Portal bridge and other NEC projects will end up being paid for in part by federal loans, RIFF, TIFIA, or whatever. But it will be DEBT that will have to be paid off with INTEREST over the next 20 or 30 years. Which could become a crushing debt load, if Amtrak or an NEC authority/Commission is not careful - or a couple of powerful Governors push for the NEC to take on more debt, so they don't to pay more out of their transit budgets because they have higher political ambitions. Take on too much debt, and someday, the choice might have to be between paying for basic track maintenance or servicing the debt on track infrastructure. Then Amtrak would have to go to Congress and the states, hat in hand and ask for help. Debt on rolling stock is a different matter because one can figure out how much revenue the Acela or coach cars are generating. Not so simple for new tunnels under the Hudson river or bridge in NJ used by both Amtrak and NJT. RIFF loans are no panacea, although as I said, I expect low interest federal loans for infrastructure are in the NEC's future.