Can I use silicone to waterproof an RPE liner penetration?

You should not rely on silicone alone to seal a pipe through a liner—it will almost certainly leak. Instead, you need to use a Bulkhead Fitting Threaded, or a Pipe Boot Kit. If you're running a pipe through a liner, and using a bulkhead fitting, the fitting should come with a gasket for waterproofing from the inside of the tank. From the outside, thread and tighten the locking nut, without overtightening. You can then connect pipes/hoses to each side as needed.

When installing a skimmer, we suggest running a continuous, even bead, of pond-safe silicone sealant around the skimmer’s front opening or faceplate flange—just inside the screw holes (use silicone over top of the screw holes). Avoid gaps or breaks in the bead.

A good option for this is Atlantic RTV Silicone Sealant, or a 100% silicone sealant designed for aquarium environments.