Thosha That's a very good question, and not small at all. So I will try to give you a serious answer.
Balanced against delaying monster encounters for the benefit of other characters not yet in the game is the deferral of expertise and skills that may be needed for other immediate tasks and opponents. You are looking at the desert monsters in Megail's quest, and deferring them. But, not getting that experience when first available may make things like 3rd Arclent War more difficult. Some parts of 3rd Arclent War could be quite difficult if Varia, Hilstara and Carina have less experience and skills. It may make the early Tower expeditions in Chapter 4 much more difficult until Riala joins as a combat character. Only you can determine that, which is why you doing a new runthrough is important.
But for my part, I like the statement you make in your playthrough which goes, "Always immediately kill all monsters unless it is said not to". It's simple and clear. I like your existing guide on when avoid encouters.