Yea, the difficulty with autotargeting any train is that in the turret's logic a "ship on my planet"
always takes priority over "ship not on my planet" (or, in the case of an incoming Wave, "ship that doesn't even exist yet"), so it's quite possible for a train to come wandering in 3 or 4 seconds before a wave and when the wave comes in all your snipers and lightning turrets are reloading. Personally I preferred the no-auto-target-trains approach
But there are good reasons for wanting them to wear down the turret trains without human intervention, so it's tricky.