I'm not sure about the bay area dealers. I go to a small dealer in Woodland, CA (just outside Sacramento) when I can (they aren't open for service on weekends) - they seem to be pretty mod friendly from what I can tell (but I haven't had any major issues to know for sure), but that's probably too far of a drive for you. Good luck - a good dealer is hard to find!
07 Jeep Green Rubi Unlimited, auto
Mods: Tuffy Cubby Storage Cover, Rugged Ridge grab handles, Shrockworks Sliders, Rock Hard Engine / Gas Tank Skids, Rhino-lined tub, Kilby Evap Can Relocation Kit, 16x8 Centerline Wilderness Series - Falcon Rims, 285/75/16 Interco SSRs, OME 2" HD Lift, PSC Diff Covers, Superwinch EPi 9.0, BulldogFab Rear Bumper, RedrockFab Front Bumper and skid