It?s funny to hear all of the different opinions. Basically, there is really only a few wrong ways to do this, but many ways that work fine. It?s really a matter of what you are comfortable with. The whole electrical system, imho, doesn?t even need to be considered until you are almost done with the finishing kit. I run conduits and don?t install a single wire until the airframe is complete. If I can run a wire in a finished airframe, I know I can replace/service that wire in the future. You have no idea how many planes I have worked on that have wires and components installed in a way that they cannot be serviced. There is always a chance that a wire may need to be replaced or removed down the road. This goes for components as well. If you can install them in a finished airframe, you can pull them out as well, and there is almost a guarantee that they will eventually need to come out.
I am personally in the camp of booting up the EFIS before engine start so I can see engine data, and so the alignment process (which is mostly imperceptible with most modern EFISes) is complete. I really don?t even consider the alignment process unless I?m in a plane with a GRT EFIS. I am a big fan of a backup battery, the Dynon battery in a Dynon installation and the TCW in other installations. I often install a second alternator because the customer wants that peace of mind, but I rarely install a second bus or second big battery. Most systems I install draw a total of less than 10 amps with lights off in flight, and in the case of an alternator failure that can be cut in half fairly easily.
Again, there are a lot of ways to do things and very few of them are wrong. As always, there are risks in every situation, so I try to find a way to eliminate as much risk as possible with the most bang for my buck and the least amount of weight without going to extremes. Planes have been amazingly reliable for lots of years. Yes, the modern electronic systems are more reliable on battery power than systems used to be, but I think the ratio of electrical system problems is hugely lower than the number of vacuum system failures. We are replacing and removing vacuum systems almost weekly in our shop, and very seldom have to replace a master solenoid, master switch, EFIS screen (because of failure), etc.
I think you are doing the right thing to ask the question, but once you read all of the opinions, do what makes you feel comfortable. If I were building your system, I would do it the way you want it, but I would offer suggestions based on my experience during the process.