On Virginia-class subs, the EOT has been made into a linear button array. It’s arranged in logical order (All Ahead Flank at top, descending to All Stop, then down to All Back Emergency; there are small gaps in between Ahead, Stop, and Back groups), and the button flashes when an order is received. There’s also an audible alert, of course.
The throttles themselves are small hand wheels, with the astern wheel being smaller and offset from the ahead wheel. These send redundant signals to the main engine controllers (which also redundant), which ultimately control the main engines. In the event of an emergency, there is a manual override station between the main engines – this is outside of maneuvering, and would require a different watchstander to man, since the propulsion plant operator is also running the reactor.
To your main point though, yes, a checkbox is inadequate. Physical controls are generally superior, which is why car manufacturers who moved away from them are starting to move back.