"You cannot easily manipulate items in the left-side list"

You can select multiple items when you hold "strg", like in any other app.
Then you can set flags for all objects for example.

For duplication offset: You can set it in the preferences to 0.

Sorry, but for 50% of the complains you get a RTFM from me. wink
But at the bottom line you´re right, there are some annoying little... surprises in WED.

I´m crying out loud on a regulary basis, too.

no science involved