1 year late, but maybe someone will google and will find this.
Im playing with 1.44 reinforced alert.
The TLAM missiles need to be programmed via the self destruct nm input field if you are using waypoints, and you need to use waypoints for your tlams here.
So by default they explode midair when reaching the first waypoint because the field by default says:
You can change this from 0001 to 0004 depending on which waypoint you want them to detonate at... in midair. Yeah. I guess it should activate when reaching a designated waypoint instead of just exploding in mid-air, but in 1.44 its bugged.
If you enter 0005 however, the missile will briefly activate after every checkpoint, and proceed to the next checkpoint if it doesnt spot any targets. This is what you need to use. Just make sure you place your last waypoint few hundred yards in front of your estimated target. It's possible to destroy factories with this method.
HOWEVER. This mission is impossible to complete without cheating and using "show truth" in map settings. Mission requires you to destroy 4 factories, however you are given coordinates to only 3. Yeah. Given how "amazing" first 2 missions were i think im done with this campaign.
P.S I don't know who thought it was a good idea to use TLAM self destruct field as an input for tlam's firing modes, but hey, modders. I guess its assumed that we read the weapons manual (its a new manual that you can find in game manual directory if youre using Reinforced alert)