I am confused by your question
To invade a colony, setting "Never Invade" makes sure you won't invade. Use invade when clear, or the other option (invade immediately?)? I prefer the last one. It may help to set troop transports to "never flee" to have them do suicidal runs to drop their troops rather than try to turn around and get shot down aiming the wrong way. And by making them invade immediately, they won't delay invading when single enemy ships arrive, finding themselves soon to be dead by the assault fleet that busted the colony defenses.
Troops do nothing in boarding action. The assault pods provide the boarding strength, habitation modules and boarding pods give defense against boarding. I would not put assault pods on troop transports, but rather on some custom swift guys good at blasting shields and closing the distance. I suggest swarms of such guys to capture ships, pure fleets with only one kind of ship (the capture ship type).
The stance of the troop transports have nothing to do with boarding action, boarding is not related to invasions.
Disclaimer: It could be that troops helps with preventing the troop transport form being captured, but in the greater scheme of things, this is rather irrelevant.
My preferred way to invade:
1: Troop ships in separate fleet, with another military ship as fleet leader. This ship should not be able to carry troops.
2: Troop ships are "invade immediately" or something to that effect. They are "never flee". And if I have a hand in design, they carry no weapons to avoid them confusing themselves into combat.
3: Start attack with a proper battle fleet on attack vector to colony or some colony defense infrastructure. This fleet should have no troops at all, troop transports do not belong in fighting fleets. I normal situations, troops should not be carried by fighting ships either.
4: Have the invasion fleet (troop transports and leader) parked in a system nearby. In my case usually at the same resupply ship (or colony) where the battle fleet left before their attack.
5: When the attack fleet has some head start, tell single troop transport (drag or control-click to select) to attack the colony. The aim is that the defenses should be dead before their arrival. Single enemy ships, or small fleets, may appear, thus the "invade immediately".
6: The invasion fleet leader does not move, he sits in a safe spot (resupply ship, colony, or empty system).
7: When the spaceport defenses are dead, I tell the attacking fleet to blockade. It should make sure they stay around and that the enemy won't land more troops. And give space superiority bonus. Usually many ships arrive at an important, newly conquered colony. They had refuel missions, or some attack missions they thought would make a difference. It is entertainment for the blockading fleet.
8: When the transports drop their troops, they will wonder "what to do?" and notice that they are not at their fleet leader. They do the sensible thing and move to the fleet leader, who sits in that safe location. It gets them out of the way, and not involved in future battles around the colony.
The "follow leader" behavior of fleet members is very useful in many situations. Tell that single, low fuel, ship to refuel. He will go off to a nearby mine, and return to leader. Tell a fleet member to move to nearby "hidden ship" location to trigger it, he will move back. Just make sure you don't ask fleet leader to do this, since that will make the rest follow and they stay there. And don't order the fleet to do anything with a member on "special mission".
If you need to move the invasion fleet, while transports are on their attack orders, just move the fleet leader. The transports on no mission will follow, and the ones with a mission will move there once the mission ends.