A library reported this. I have not investigated properly, but grep'ing for the syspref in C4/SIP/ gives no results. I would say this is surprising. Either the old syspref should apply to SIP2, or there should be a separate syspref like CalculateFinesOnReturnSIP2.
It looks like the pref is checked in AddReturn, so that could explain it not showing up in SIP code.