Regarding automatic tool switching, one I'd really like to see is automatically selecting the flag tool when you click a flag type in the top right
People with actual mice (rather than a laptop trackpad) are more likely to also have the control to scroll to the flag type they want, so I think automatically switching is a reasonable default (additionally, flagging a tile does not reveal hidden information and is therefore a fundamentally reversible action; I accidentally lost a probe earlier to forgetting to switch to the flag tool)
I think FreakzWasTaken's idea that the solution is to make it more clear what is about to be done is definitely the right approach, could I suggest putting a preview of the active tool (perhaps at 60% opacity) in the cell when preparing to take an action (i.e. a semi-transparent probe/disarm/flag icon in the cell currently hovered