I don't think timed prompts would mesh well with the game flow. You'd have to pause the game for 2 seconds to wait for user input whenever reaction is possible. It also adds a real-time element to turn based game.
So what you say is, that it wouldn’t mesh at all.
Surely, better then trying to implimented some whack-a-mole minigame for reactions it would be just to keep original system with pop ups, as in Solasta.
Luckily, no matter if current Larian’s implementation works or not, player will have EA to try it and provide feedback. As I am not familiar with DnD5, I cannot effectively speculate on the subject.