The rationale of this rule is to prevent "hide-out" plays and the such. The wordage used to read : '...must leave immediately". The concern was immediately means quicker then quickly. Many Big Ole' Bubbas don't often react quickly to much. Immediately was then changed to 3 seconds. I don't believe we need a stop watch to time this as long as the replaced player is leaving shortly.
If a coach burns a TO while you're counting his players, he beat me to the draw AND no hide-out or trick play is going to occur. While some might
after the TO was called, I wouldn't. If the opposing coach inquired, I'd respond : "Coach, he saw a problem and fixed it at an expense of a time out while I was still counting. He gained no advantage and I'd treat you the same if it occurred to your team."
DISCLAIMER : This is only my opinion.