Here is a 2006 Boxster 6 spd trans.....
and here is a 2009 Boxster 6 spd Trans
And here is a 2017 991 Turbo S Motor.....
So the change in Bolt Pattern has come with the DFI Motor introduction in 2009.
AND, note this motor now has a 10-Bolt Crankshaft.....earlier models have an 8-Bolt Crank.
Len