Yes, those installers predate RPro. The only time RPro grabs programs from the legacy folders is during its installation. Any changes to the legacy synth programs must be copied by hand.
FWIW, the Rapture Classic installers that ship with RPro include the 2 Rapture Expansion Packs. At leasat the Expansion Pack programs I searched for showed up in both the Rapture Classic Factory Library and User Imported Library.