[TomTom]

Alas there are no easy cvars to change.

Some minor improvements may be possible from the waypointers revisiting the nav file. Crapshoot indicated that engineers are more likely to fight while they are in the route system on their way to important objectives. Of course if they fight they won't likely re-enter the route system so this improvement is sort of a one time willingness to fight after spawning until the objective changes. I have really not verified this but did try chaining routes in one map JIC.
The other thing to do as the bindlestiff documented in the wiki topic "the route system" is to try to get other bots to run along the same routes with the engineers. There is no way to make the bots specifically cooperate so whether the bots do accompany the engineers is 1 part Monte-carlo and 1 part restricting the bots' options in the waypoints. Since you indicated that you were changing the bot composition of the teams playing you may affect to some degree the frequency of such accompaniments (either way) depending on how the waypoints are done.

BTW in my experience, besides engineers navigating to major builds and dynamites, any bot navigating to a steal action may sometimes also be reluctant to start a fight. Typically in either case the bot will fight back after receiving substantial damage if they are not actually building or planting at the time.