On the nice airplanes, we build seals around all of the panels that are routinely opened. It is call a "Form-in-place seal" (FIP Seal for short). We put something similar to mil-s-8802 sealant on the inside frame, cover the inside of the panel with petrolatum, and shut the panel. The seal forms due to the pressure of the panel, and it will always be a perfect fit. After closing, we clean the excess away with a plastic spatula or putty knife. Depending on where the excess happens to move, you may have to make a couple of passes here. Anywhere where you can get the sealant to stay on will be a good place to use it. Just a note, it will get in the way of rear doors if you plan on using it at the rear of the front door. The website listed gets into it just a bit. If anyone else can provide some insight here, it would be appreciated. I'm just an Ordnanceman.
Sealing Compound MIL-S-8802
P.S. - This holds up to approximately mach 1.5 and aircraft washes. You can paint it, and its pretty permanent, but can be scraped of with a bit of work.