3) I think that Automatic Upgrade will upgrade the Ship Designs. Manual Retrofit would then mean that the AI never upgrades them. So you have new AI designs, but none will ever be retrofitted into them, unless you asked.
4) I think Manual Upgrade, so no new AI designs. Once you do make a new design, they will Automatically Retrofit.
But I have Fully Automate Ship Design in Research and Design section of the Empire Policy Screen, with some military ships unticked.
It says that Ship Design must be automated for designs to be automatically upgraded.
I never had starports changing types before though, but I rarely build medium starports.
I've never seen ships retrofitting when they are never supposed to, and I play on Manual Upgrade with Automatic Retrofit. Unautomated ships never automatically retrofit, and as for automated ships, I have no idea if they do or not.