"With another activity to keep exploration from getting stale."
punch me in the face while I eat so I dont get bored
"Even though the exploration parts are designed with this in mind?"
This makes no sense. You are perhaps insinuating that exploration parts are dumbed down in order to take random encounters into account. But first of all, this means that by not having random encounters we could have richer worlds to explore. (not like that matters in an RPG right??) But it also means that if you design environments with the existence of random encounters in mind (which logically means dumbing said environments down) then it stands to reason that by taking that logic to its ultimate conclusion you would decide to have no environments at all. Which is basically what SRPG's do. I'm saying, stop trying to have your cake and eat it too. You can only either be fighting enemies or navigating the environment at a given time. No matter what in a game with both, you have to take turns, and out of all the ways one might have tried to make a game that alternate between these two subgames, why choose the stupidest method possible? If you had two movies and wanted to watch them, 1) why would you alternate between the two in intervals of seconds at a time, and 2) why would you make the intervals RANDOM.
Also, only now I just realized, you didn't actually refute my point. You didn't argue that encounters were somehow good for exploration or somehow didn't make the environments suffer. You just said that they are "designed with this in mind" arguably in the same manner a urinal cake was designed to be urinated on in mind.
"Pokemon, Dragon Quest, Final Fantasy; all games that benefit from these random encounters."
What does this have to do with atmosphere? Furthermore, random encounters disrupt atmosphere by definition of the word atmosphere, so it would be a desperate point to argue against. If you disagree, why not have random encounters during cutscenes then? What fucking difference does it make, at this point?
random encounter in 3... 2...
"Sometimes yes, sometimes no." <--- Sometimes spoiled chicken gives me stomach virus, other times no. So it's not a bad thing by virtue of the consequences only sometimes taking effect.
"Depends on the dungeon, honestly, and this might have a little more to do with visual direction (IE being able to differentiate your environment)." <--- Translation: "Random encounters are so godamn important, that if need be, all environments should be linear corridors with low graphical detail in order to minimize the invariably resulting confusion of the random encounters. Of course, the easier solution would be to just have the encounters not be random, but that would be admitting that random encounters are sort of objectively shitty, so that solution is out of the question"
"It's usually a small animation to signal a transition into battle." <--- it's like someone fake-punching you, and you flinch even in cases when you knew they were going to do it. Because you didn't know when. How many times have you walked up to a treasure chest, finger all but wrapping the X button to open, but BAM "haha nope. Enemy first" Damn it, you startled me. God damn it.
Furthermore, the transition animations tend to be visually and audially assaultive and unnecessary. You dont get visual static and hear sound effects of tearing up paper whenever a cutscene starts or whenever you enter a shop/inn, bring up a menu, etc. Which perhaps says something about the nature of random encounters existing at all.
p.s. do we even agree on what the word objectively means? Because as far as I can tell, no matter what objective parameter could conceivably exist for judging a game (or any piece of media for that matter), random encounters do not help. They serve only to be a taint on the experience, and that's just the best case scenario.