I don't understand the argument that reactions interrupt the flow in a turn based combat system. If it was RTwP, then I get it but turn based is methodical by nature.
The biggest argument I can think of is for multiplayer. Reaction pop-ups will result in many more times where most of the players are forced to wait for a single player to make a selection. Thus, everyone would have to pay attention to the entire combat and not just their own turn.
But honestly, this isn't a very compelling argument. Is it really the worst thing if, once in a while, you have to wait like a minute or two for your friend to come back from getting a snack?
Finally, here are many ways of addressing this: -Allow the option of toggle or pop-up reactions -Add a timer to the reaction pop-up window