a easy solution to me seems to be cut the make a slice in the liner and use a water proof zipper sew it in and use the stuff for tent seems to water proof the seem.
cool idea - go for it. a good tailor would be able to handle it. be aware that when you slash a piece of fabric to insert a zipper, you need to also cut little 45 degree extensions both sides, each end, to allow the fabric to fold back to create seam allowances to sew the zipper onto. each corner will be a weak point. the solution is to use a separate piece of fabric to create a 'window' (kinda doubling up the system) - the tailor will understand. use coated fabric so the raw edges do not fray.
i doubt you need to seam-seal the system. first try without, then deal with it if you get leakage.