>Hard to believe but I think some eastern railroad(s) use a yellow to indicated "Proceed at restricted speed"

Speed signaling, and it's a red over yellow pot called "restricting", which isn't supposed to be confused with a red over yellow high signal, which means something completely different.

>and in Chicago an Amtrak train rear ended a freight after passing a yellow signal according to reports.

Correct, and it was that red over yellow pot meaning restricting.

>Not a great idea to have such a variance in rules in one country's railroads. If you've seen a yellow all your life as a signal that indicates the block is clear to the next signal and then end up running on another railroad this can be trouble.

As long as you operate on a speed-signaled or a route-signaled railroad only, no problem. It's moving between the two which can cause confusion, leading to things like that P-42 on top of a double-stack car.

>I remember right after BN replaced yellow/red flags with yellows an engineer blew by a red flag.

It may have been the other way around because the yellow-red flag business is part of the FRA's roadway worker protection regs, and they are hot about the subject. Yellow flag = slow order, yellow-red flag = gang, with or without a red flag.