Starting the game for first time,

it prompts you to select a room and place a spawn.
This is fine for a lot of beginners and people who like to place the structures manually,
but I'm not one of them and would rather solve that problem programmatically.

I personally find it a bit of ironic that the first action of a game about automation is to force people to manually set a position.
Hence I'd like to change that.

It would be much nicer to only claim the room first and make the first "spawn construction site" free.
If your script isn't able to do that you can still prompt the player to place the initial spawn construction site.
(Something along the line: Do you like to place a spawn? OK / dismiss)
You may loose a tick or two of the safe mode with this method,
but I think that is a small price in comparison to the ticks your script has to use in order to move a suboptimal spawn position.

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The main objection I've seen to letting people's code place the first spawn were the server load of providing vision to all rooms so that a script could claim a room and place the spawn.

This proposal sidesteps that: Someone claims a room manually, the controller starts ticking down as usual and if they don't get their basics sorted their script will stop running when the controller goes back to neutral.

Alternatively, it could be a setting in a player's account settings. Something like "Respawn method: Claim Room / Place Spawn." That way nothing changes for players who aren't at the stage of high automation.

The message could still be claim a room and after you claim it could go to "place a spawn". An automated code could hijack the spawn placement message. Manual players could just place it.

So claim the room, code starts running (if there is any), then ifs first to place the spawn wins either manual or code. The only diff from a noobs pov would be having to "claim the room" rather than just navigate to one. But I don't think a "claim" then "place" would be too much extra work.