Editing a footprint: if I deselect all the layers but the active one a drag selection still selects top layer pads? 
Is it just me or is this a bug?
Note: the two pads shown below were hidden before I selected a few lines in F.Courtyard with a rectangle
Running version 6.0.2 on W11pro
Sound like a bug to me.
But you can still achieve what you want if you go to the objects tab and make the pads invisible.
Hope this helps.
I agree with @der.ule that this is a bug.
To give you another solution for box-selection on only one layer:
Utilize the display-modes Normal - DIM - Hide.
The display-modes show not only another view (with less distraction) but with Dim/Hide all the selection works only on the active layer.
So for your task: set F.Courtyard as active, set display mode to Dim/Hide, box-select (or CTRL-A for select all).
Display-mode changing with icon on left toolbar (only Normal/DIM), inside the appearance-manager or with hotkey (frequently used, works best for me)
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