Its possible to do so although getting it to work is a bit hacky thanks to just how bots are really eagar to spawn in with intel when possible. Very much possible though as shown by security.
Robots win when they get your intel to their train (blue metal box with a hatch on top) Includes modified version of mannhatten_adv2 mission to test functionalites Special thanks to Idolon for creating inspiring geometries! IMPORTANT: mission...
tf2maps.net
IIRC the main gist of the setup relies heavily on pre-requsites and having the bomb be spawned in on demand via a point template. You use 1 bot in a OOB dev room to hold onto the actual base bomb just to avoid hud breaking. Every other bot should be following a nav prerequsite instruction to go to where you want bombs to spawn from. When they get there you can spawn a fresh flag which one of the bots should hopefully pick up with a point template. After pickup a quick fix to the bot instructions either through another prerequsite or changing the bots default behaviour would be needed as otherwise the bots will just decide to either still go to where the bomb spawner is or just hunt for players.
Its a bit convoluted but its the only way to really do bomb setups like what you are describing since default behaviour is to always attempt to spawn in with whatever intel entities are found present in the level, they have to be spawned in dynamically and that requires a lot of extra entity work to get them to understand where to go as well.