Both of these items are as designed. In both cases there has to be an out for automatically running an action.

If you drag files to the dock icon as opposed to the main window, the default action will run. You can also place a Droplet on the desktop and drag to it as opposed to the main window. That even has the advantage of letting you set a specific Open Mode.

As far as running the Auto Save action, it's pretty much the same story. An easy out is necessary. Further, Saving from the FIle menu is entwined with the action based Save mechanism. Doing the auto save here would be extremely convoluted.

If you want this specifically for Save Selected Files if Modified, create an action as follows:

Test if property 'Is Modified' is true (Set test state and Variable 0)
Run action 'your default action' if Variable 0 is true
Save selected files if modified

If you want it for Save Selected Files Always do the following:

Run action 'your default action'
Save selected files

In the Action Manager assign the created action to a Toolbar Action Button. Place the associated icon (which you can change) on the toolbar. Use the created toolbar button.

I understand that these are workflow changes but quite frankly changing the behaviour for either of these items would require a ton of changes. 🙁