Simplify handling of DD bonded distances

Simplify handling of DD bonded distances

To simplify and clarify the DD setup code, we now always always store
the systemInfo.minCutoffForMultiBody and use a separate flag to tell
if we should increase the cut-off distance for bonded communication.
There is a minor behavioral change in that with large domains and
bonded communication filtering or DLB, the bonded cut-off is now
5% of the bonded cut-off longer as the margin is now included.
This has a negligible effect on performance in all cases.

Change-Id: Id409353c517181ac56e8d3f1f36c22c705aa8077