I'd be tempted to use an edge-locked plain stitch* first (with an overlocking machine, ideally, or edge-locking stitch on a conventional machine), and then sew this down afterwards; then you have three layers of fabric, rather than four with a flat-lock* seam. It's also easier to make.
This construction method is commonly used in commercial softshells.
And no, I see no point trying to seal the seams, or use waterproof zips, when the fabric itself isn't waterproof (manufacturers, please note...)
* must have been away with the fairies last night: I meant plain seam and lap fell seam.