You have to manually spawn the flag after the round starts. Make an ent_template (or something similar i dont remember the name) for each flags. Place them where the flag will spawn and target the flag to be its template. When the round starts, send an output to the ent_template and ForceSpawn the template. I think thats the correct name for that input.
No the countdown is created by the arena logic entity. No matter what you do it will do a countdown I think. Even if you send no output with the arena entity, it will do a countdown.
edit: Love the detailing! Its a bit simplistic, but I'm a minimalist so its perfect. Though I did find a little problem you may want to look at: The fade on these windows are a bit extreme when far away, maybe tone the colour down just a bit
These spawns are hella S E X Y, but I have a suggestion for the blue one.
Look in the black circle. That place is kinda empty. I would suggest just putting a horizontal window there. Like the barn blitz one.
Otherwise, very naise. and also, (open at your discretion) a secret!
While checking the blue side, i noticed something. It had been bugging me earlier, but i finally now know what is was.
This important part of the 3D sky box is covered up:
Maybe you can either delete the displacement, or make it smaller.
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