I'm fine with the idea of a main panel with only 2 things in it feeding a sub-panel with everything in it.
Question #1 - I'd rethink putting a service panel outdoors at all. Weather is rough on panels, even if they claim to be outdoor rated. I'm a little nervous about a 100A breaker supplied from the normal bus bars, but if the manufacturer stands behind it, okay. The 100A wires are going to be a mother to wrestle onto that 100A breaker. Are you quite sure the power company has provisioned you 125A service? 100A is more common.
Question #1 (the second): You're gonna want more slots than 24, since this box powers pretty much your whole house. Nobody ever installed an addition and went "Gosh, that job was sure made harder and more expensive by having too many slots in the panel". It's a false economy, especially since bigger boxes are often bundled with more breakers. Your house may be ok now, but do a kitchen remodel and lookout!
Question #2 (the second): Don't bond your grounds to random plumbing that happens to be going by. It's not code, and someday you might have a plumbing problem and the plumber replaces a downstream chunk of it with PVC. Whoops. Also, they've been upgrading customers to PLASTIC water meters. Double whoops. Bond properly and to code.
Question #3 (the third): Bond ground and neutral only in the (singular) main panel. As such, you need 4 wires between main and subpanel.
Just for your edification, it's only a sub-panel if it's fed from a main panel. If it's fed directly from a transformer, it's a main panel.
You don't have to bond the conduit if it's only there to "provide support or protection of cable assemblies from physical damage", according to 250.86 ex. 2.
National Electrical Code 2014
Chapter 2 Wiring and Protection
Article 250 Grounding and Bonding
250.86 Other Conductor Enclosures and Raceways. Except as permitted by 250.112(I), metal enclosures and raceways for other than service conductors shall be connected to the equipment grounding conductor.
Exception No. 2: Short sections of metal enclosures or raceways used to provide support or protection of cable assemblies from physical damage shall not be required to be connected to the equipment grounding conductor.
Best Answer
I have used many panels just like this I usually don’t move the buss but it is easy to do the 2 screws are usually 10-32 self forming screws that hold the buss in place move it if you would like, code has no requirement on the position.
If you can’t or don’t feel comfortable with that location move the buss. I always have a set of drill/taps for box modifications they drill and tap in one quick operation if using a tapped hole it’s a lot easier to put the screws in and code legal with a 32 pitch screw.
Never use self tappers inspectors look for those and will red tag a job if they see one. Self forming machine screws are different and have the 32 pitch most commonly 10-32 but I have found some 8-32’s used by different mfg’s.