ok, i prefer to drill my pipes through the joists, but if its code compliant where you are, in your type of construction to just clip them to the joists, then that will make it much faster/easier. It also makes it even easier to run all your pex lines ahead of time, then do the switch over after. It also makes the homerun system much easier to install, you can just run a bunch of cold water lines right next to each other with one big clip/strap holding the whole bunch up together. I generally prefer to keep my hots separate from each other and insulate them individually, this makes the hot water get to each fixture faster with less heat loss to the air and the other dormant hot pipes.
You could have the entire system run, clipped up, etc other than the main line to manifold connection and the individual fixtures (just leave extra pipe hanging under house until ready to swap out the galvanized), and switch the whole system over pretty quickly with minimal down time. And this shouldn't cost that much more than the trunk and branch system - a lot more pipe, but pipe is cheap. A lot less fittings, which are less cheap and a bit of labor savings.