No. Whatever the unknown unknowns are, they're not going to be that hard to work around. Keeping track of a few train cars isn't exactly the Manhattan Project, even if it has to be done underneath Manhattan.
The video suggests that the total budget for the CBTC retrofit was in the vicinity of $1 billion. I hope that I either misinterpreted it, or that the budget includes other improvements, because I doubt it cost that much (in 2018 dollars) to build the initial subway routes in the first place.
Look at it this way: why do you suppose your suggestions haven't been implemented yet? Do you think the vast array of parties with skin in the game haven't thought of them (and are thus incompetent)? Do you think they simply aren't motivated to implement them?
I think the vast array of parties with skin in the game have treated said "skin" as a target for optimization in itself. I'll readily admit they're likely better at that game than I am.
