Bluetooth: Controller: Use local variable for current PDU's flags

Use local variable to update current PDU's Common Extended
Header Format flags instead of updating it directly in the
PDU buffer. This is required to be able to non-destructively
be able to manipulate the PDU's header flags and contents
many time before a final commit of the updated PDU.

In order to calculate overflowed AD data length, PDU is
manipulated couple of times to determine the overflow length
and next to be able to add aux ptr field when chain PDU is
appended.

The changes are now consistent with how Periodic Advertising
PDU's Common Extended Header Format is manipulated.

Signed-off-by: Vinayak Kariappa Chettimada <vich@nordicsemi.no>