Plumbing in Panels
You reduce plumbing problems in panel construction the same way you do in conventional framing: place all plumbing supplies and vents within interior walls.
Where placing a vent inside an exterior panel wall seems unavoidable, you can order the panel with a pre-cut chase to accommodate the required vent stack. Just remember to pre-cut the top plate over the vent chase before you attach it.
If it turns out you should have ordered a panel with a pre-cut chase for a vent, it's not recommended that you cut out a chase on site, since that usually involves cutting panel facings. As an option, you can frame out a small chase up against an exterior wall; this costs a little space but saves headaches. If you must cut a panel facing on site, don't cut the top one or two feet; doing so would eliminate the panel's strength. If an uninformed plumber's helper ends up completely cutting a facing from top to bottom, you should try to insert a spline behind the surface of the cut in order to reestablish the panel's strength.
Where plumbing vents penetrate roof panels, take extra care to prevent warm house air from leaking up into the panel. Since plumbing vents expand and contract, they can break foam sealants. A better tactic is to use an EPDM sleeve. Cut a piece of sheet EPDM material large enough to cover the bottom side of the panel penetration; then cut a hole in the EPDM large enough to slip it over the vent pipe and slide it down the pipe to where it can attach to the underside of the roof panel. Then push the pipe up, position the sleeve as needed, and attach it to the bottom side of the panel. Staple and caulk the sleeve for a finished seal.