When you added the new system did you update
shortest_illegal_path.ini
shortest_legal_path.ini
systems_shortest_path.ini

Thanks for keeping it running

The door open sound while undocking from a base would be in the thn file (since you are still in animation). You would have to add it and provide the trigger.
There would be a secondary problem of 'ducking' involving the normal launch voice, but both could still be audible.

Oh, forgot you run a mod that players can join without the mod.
Here is the declaration:

[Solar]
nickname = co_base_ice_large02
ids_name = 1
ids_info = 1
type = STATION
DA_archetype = solar\dockable\co_base_ice_large02.cmp
material_library = solar\Solar_mat_co_base.mat
LODranges = 0, 20000
mass = 10000.000000
open_sound = depot_open_sound
close_sound = depot_close_sound
docking_sphere = berth, HpDockMountA, 2.500000, Sc_open dock1
docking_sphere = berth, HpDockMountB, 2.500000, Sc_open dock2
docking_sphere = berth, HpDockMountC, 2.500000, Sc_open dock3
docking_sphere = moor_medium, HpDockMountD, 5.000000
docking_sphere = moor_large, HpDockMountE, 10.000000
docking_camera = 0
solar_radius = 500
shape_name = NNM_SM_DEPOT
hit_pts = 999999961690316250000000000000000000.000000

Your capships will undock from D and E (but this depends on what you have changed from vanilla). My mod is highly tweaked, I allow capship docking on bases and made special docking arrangements for them that may not work on your vanilla setup.

Best thing I can say is experiment and keep a vanilla backup if you need to revert.

As you noted, capships, no matter how they dock, can indeed UNDOCK from the berths (unless you have gone to extraordinary length to lock them into moors). This is why you are getting hung up, probably on the door or the controller window. I use fast docking and extended ranges and special docking methods, see what works best for you.

The dock points you referenced are correct, I had them reversed them in my first response. Fixing that now...

Run datastorm, the errorlog will show you what half of those errors are.

One possibility is if you set your npcs to use bots and batts. They can use them very efficiently. If you have given them, say, 5 batts, their shields could easy stay up for 5-15 seconds. Scan them to see how they use them.

Wow, you constantly amaze us adoxa