Except that it's really not save by DM intervention. Remember the original case that I quoted above that generated this line of the discussion. The two guards designated for the encounter get bumped off ahead of time. Barring intervention (or plausible game events), those guards aren't supposed to be there. The setup you proposed, that the guards were designated for the throne room encounter, makes the counterfactual the reality prior to intervention to preserve the challenge of the encounter.
The whole gameworld is only a consequence of DM intervention. There is no particular way that things are, or are not, supposed to be.
In one sort of game - what I think of Pulsipherian/Gygaxian play - then there is an expectation that the players will, by their choices, influence the difficulty of subsequent encounters. The players are expected to work out - using scrying magic, say, or thief skills - how many guards are in the throne room, and then to do stuff - like ganking the two guards who leave - in order to make the throne room fight less difficult. In this sort of game, for a GM to restock the throne room after the ganking would be tantamount to cheating.
But this sort of Pulsipherian/Gygaxian play is just one approach to the game. It assumes that operational planning, scouting, etc are crucial to play. It downplays the actual encounter as a focus for play in favour of exploration on either side of it - planning beforehand, looting afterwards. In the OP I described a different approach to play, which emphasises the encounter/situation as the focus of play.
What I've been talking about is players affecting the challenge of future encounters by their own in game choices.
And what I'm talking about is an approach to scene framing in which this responsibility lies with the GM, not the players. In which the function of player in game choices is to generate story/thematic consequences - "Hey, we ganked two guards" - not mechanical consequences - "Hey, the encounter dropped from EL n to EL n-1".
Then why not let the PC's effect on the throne room encounter, by bumping off the guards, have an effect if mechanical balance is rarely an aspect of honoring earlier story choices? How exactly are you honoring their story choices if you aren't letting them cause downstream effects?
I think that you are running together here what I am trying to keep separate, namely, story consequences and mechanical consequences. If the guards have been bumped off then the guards have been bumped off. That is part of the fiction. The PCs can walk into the throne room and say to the guards (for example) "We've already killed two of you - do the rest of you feel lucky, or do you want to surrender?"
But this content of the story is a distinct thing from the mechanical balance of an encounter. The story of the PCs as guard-killers is independent of the number of guards subsequently in the throne room, or the existence of a secret pit trap in front of the throne.
Or are they doing all the work of patting themselves on the back for bumping off the guards? My assumption wouldn't be that they wanted to just have another couple of kills or to show off. My assumption would be that they wanted to actually accomplish something by bumping off the two guards.
But they have accomplished things. For example (assuming they took the guards out quietly) they've prevented the alarm being raised. This changes the character of the throneroom encounter (for example, it won't involve dealing with a hue-and-cry - which changes the dynamics quite a bit - for example, if there is a hue and cry then the PCs can no longer reach a deal with the king in which their invasion of the palace remains secret).
At this point, as DM, you're the one choosing which consequences of encounters you want to value. You're hoping that you're favoring the ones your players favor, but what if you're incorrect?
But this is not a problem unique to me. Suppose I start playing in your game, and I find out that you run your game in such a way as to prioritise operational play and operational choices. And so I get bored and quit the game.
The default solutions to these sort of socia contract issues are (i) to talk about it, and (ii) to try it and find out what the revealed preferences are.
What do your players say if you ask "If your actions as PCs would make a future encounter easier, would you like those actions to have those consequences? Or would you prefer me to add complications to preserve the challenge of the encounter?"
I've never asked them that precise question - particularly as it uses "consequences" to mean "mechanical consequences for subsequent scene framing". But my players know that I set encounters so as to be interesting, and adjust levels, numbers etc in a way that will make for dynamic and interesting encounters. Besides reading my posts on these boards from time to time, and talking about playstyles before or after the game, they see me doing it at the table.