Disabling planetary defenses

Try using one fleet with multiple task forces. For the task force that has the troop transport set the strategy to capture planet. The other ships will take care of the defenses. Once the drop pod reaches the surface, they'll stop firing and leave the planet alone.

Space Empires Depot | SE:V Balance Mod

that might be the issue. It could have launched the pod, but the sim doesn't do anything after that point.

Dit you set the Ship's strategy to Capture planet in the ship design screen?
The ship still has to know it needs to land the troops.

~Myrath

This is why I control everything myself during one of these operations. No miss-steps, no mistakes, and a sweet planet without alot of damage.

Instead of just setting colony related targets to an Engage Distance of "Do not engage" for attacking colonies, would doing that and/or changing the Damage Amount to "All Weapons Gone?" have any effect or not?

I just forget about trying to take out anything that is on the planet that can fire back.

I just build a ship that can take everything the planet can fire at it, and I may destroy all ships, satellites, and fighters that may be there but I don't fire on the planet at all, and if that does not work I just destroy the planet or build many more troop ships to take it (many ships may take the planet where one does not).

There is no way I know of for setting your ships to fire at the planet but not destroy all of it.

Yeah, setting it to weapons gone will usually cause the armed ships to stop attacking when defenses with active weapons are destroyed. But, don't do that for the drop ships. Otherwise they'll not drop.

1:
The Base may have had no supply for some reason.
No supply means nothing happens. iirc, even PD weapons with 0 supply use won't work if the station has no supplies.

Are you playing SP or MP up against human players?
If against human player run empire, it is possible they simply forgot to put supply storage on the base design.
If it is an AI empire, then I have no clue beyond the fact the base was likely out of supply for some reason.

2:
Since a ship was attempting to drop troops on the planet, it makes sense that other ships would not attack the planet. I have no clue why they didn't move to attack anything else.

iirc, Fighters are in their own group after they launch, and probably not considered part of the fleet/task group, and so likely decided to go after the nearest valid target based on their own strategy, causing them to attack the base.

3:
iirc, ground battles happen in the same turn, not the next turn.
It makes sense in many ways, as when an invasion occurs, things usually go to hell rather quickly, and not at a later time. (It isn't WWI, where opposing sides would actually have troops do stuff together at times battle was not occuring. This is more of a modern 'hit the ground running and gunning' type of thing, no time to waste, no desire to wait around to see if the defender get reinforcements)

4:
Not sure.
Since the fighters attacked and the ships didn't, maybe something within the ship strategies are conflicting with task force strategies, or something with the task force strategy in general.
Someone probably has a better idea on what the likely cause might be.

1: if against a human player they might have set the starbase strategy in a weird way, thus only allowing it to fire on armed ships.

3: ground battles happen in the end of the turn you drop troops.