Depends on if you want a permanent bond or a flexible seal. Myself, I would never use RTV silicone on aluminum. Epoxy adhesives are best where you have very little flex, want permanent, and have to paint over. Urethane adhesives don't take paint well but have excellent bonding and flex. Automotive sealers are usually paintable, strong (for a sealer), and have exceptional flex. Recommend not using epoxy unless you need a structural bond. I suggest contacting your local paint supply and getting urethane panel bonding adhesive for things you want bonded and automotive sealer for where you want a permanent seal. Regardless of the brand they carry (mine is 3M), you will have products there actually intended to do the job rather than sealing a leaky window or bathtub.
EDIT: While I know they need to keep the apparent cost of building their cars down, I'm curious how the guys at FFR would feel about it if they got their prized sports car back from the dealership and found seams and leaks bonded and sealed with silicone from HD.