or is all extra reciprocating weight bad?
Mostly, yes. Unless you are chasing a smooth idle or building stationary type engines (gensets etc) But you can't race a genset!!!!

also - the B16B has a very high R/S ratio - 1.8 or higher
You are correct, a high rod stroke ratio does offset some of the problems with flame propogation through the chamber. To be specific. It allows the use of less timing and a later spark initiation because the piston dwells at TDC longer but accellerates away faster.