It’s still important to check the mixture at all throttle openings. If you run too weak in the mid range where the needle jet is controlling the mixture you can still overheat the piston and it can happen surprisingly quickly. Although the piston might not get holed it can still smear across the ring lands which can result in the rings sticking in their grooves.
As far as the silencer making a difference to jetting is concerned, it surely depends on individual engines and where the “cork in the bottle” to gas flow actually lies. Changing the silencer on my 350 from the OE Indian made one to a “straight through”Gold Star pattern made a very noticeable difference, much more than changing the inlet side. This was the same with my other bikes, dating back to my very first one, a BSA I tuned in the 1970s.

Built like a gun... could go BANG!