Code is there for a reason. Usually it's because of failure of a structure, and usually it's something that happens over and over again. Every building that is built to code meets a minimum standard. That's not saying it could be better, it's just saying that's the weakest you can built the building with a good chance of it surviving through most weather conditions.
3) Diagonal bracing is a huge thing that gets missed by a lot of hobby builders. Adding that to each outside corner will do more to stiffen your building then anything else. It's cheap, easy and very effective. OSB or plywood also work as diagonal bracing, but metal panels do not. In the buildings I've been involved with, it was on the inside of the framing so the metal can go on over the purlins without any notching.
4) Notching is going to give you the most strength you can get. In every case, it is always best to rest your loads on top of structure. Any time you span an open area, you have a weak spot. In theory, a house or building should stand without a single fastener because every piece of lumber is on top of another piece of lumber. You never want to hang or attach to the side of anything if you can help it. If you do, you need metal brackets designed specifically for that purpose. Like joist hangers. Bolts used to be alright, but it's been proven that the wood splits where the bolt hole is because all the weight is carried by that spot on the lumber, and not carried through to the entire board.
Notch your posts and then bolt them in place. Bolts are great for keeping them there, but not for carrying the load.
You didn't specify on the notching, but in some areas you only have to notch for the first 2x12 and the second one laminated to it can also act as a purlin. Other areas wont let you do this and you still need to add another board to it for your purlins. I would make sure I knew what my inspector wanted before I started.
With every header, adding half inch plywood between them and gluing them together with liquid nails, or something similar, increases the overall strength tremendously.
I wouldn't use 4x6 for a building. I've seen too many of them turn and twist after a few years. The only thing that seems to remain straight are 6x6's.
Eddie