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Manual under Auto Design (see green circle below) means that as new techs come out your ship will generally not be upgraded. You’ll need to select the design and then click Upgrade from this screen when new components are researched. You will probably have to manually manage the weapons
each time you use Upgrade as we just did on the previous page (the AI does not make the best weapon choices for.
(copy from Scotts guide V 2.3)

So far ok.

But what does the Retrofit column do if you set it on manual? What is the difference between manual and auto regarding the retrofit column
Does it mean you have to retrofit all ships or bases of this type manually even if they are set on full auto?

Yes. that is exactly what this column does.

It is usefull if you have different designs in the same role.
So your Missile Frigate does not get upgraded into a Close Support Ship.

Or your Ressource Scanner Exploration Ship does not get turned into a Explorer with Survey Modules.

Further question:

Does Auto Upgrade mean it CAN switch to different types within a class? Or does Retrofit do this?

Auto-Upgrade means the AI upgrades your ships automatically if you research new technologies.
And enable ship design in the Empire Settings.

At the current state of the game, especially when using multiply design per role, you want this feature turned OFF.
All Caps. Seriously.

Because the System is very keen on putting weapons on designs that don't need them in favour of removing stuff you actually want on a design, switching weapons around in the port, replacing components in the same category with totally different uses like it happens with crew compartments and onboard marines.