Since when can you not request docking permission when a settlement is offline? I do it all the time. Last time was less than a month ago, for a mission where I was going to the settlement to power up and steal data. I also do this EVERY TIME I get a mission to clear scavs from a base. Land at the pad, let them come to me (not a long wait) and use my ships tanky shields as a backup if they manage to hit me and drop my shields (not often).The issue is you can't request docking permission since the settlement is offline, this also implies it is safe to land since you're coming to repair/help the place.
If it is implied that you shouldn't land on the pad despite the settlement being offline and you being an ally, then I believe it should at least be written in the mission description like other requirements or warning are already being displayed.
Note that you don't even get a pad loitering warning when you land on the pad so even more reason that it is quite insidious to fine you when the settlement is reactivated.
If the pad is too small, then you can't land there. I then land somewhere nearby and take an SRV (usually a Scorpion) in to the base and park it behind a building on the edge of the settlement with no doors facing it (usually the power center).
I also routinely interact with the settlement services (usually turn in bounties) with settlements that I've just wiped out - killed all the bad guys and taken their power core. I can (bizarrely) turn in the bounties for these dead bad guys right at their own, dead, base.
If the pad is too small, I land somewhere nearby and take an SRV (usually a Scorpion) in to the base and park it behind a building on the edge of the settlement with no doors facing it (usually the power center).