I would replace the old leaking rubber gasket/seal before applying an outer clear sealant bead. Replace the rubber gasket with butyl putty tape.
The OEM rubber window gasket/seals are made to be replaced and are utilized on most RV OEM windows from the factory (both fiberglass & aluminum sided) ...., and overtime are prone to leaking.
I replaced all my rubber gasket/seals on my prior 2005 Eagle with butyl putty tape when the first window started leaking.
My 2018 Jay Flight (aluminum sided) has the rubber window gaskets/seals and the first thing I did was run a bead of clear sealant along the top of the window frames and about 2" down each side (Jayco a few years back use to do this).
2016 GM 2500HD 6.0L/4.10
2018 Jay Flight 24RBS
2005 Jayco Eagle 278FBS (retired)
1999 Jayco Eagle 246FB (retired)
Reese HP Dual Cam (integrated sway control)