Some thoughts, takeaways and questions answered...
For starters the 562XP was computer CAD designed to be powerful, lightweight and nimble in the hands of its user. Which led to the cylinder being tilted rearward and allowed for a better downward flow for the exhaust for increased efficiency. The longer muffler gives more room for the flame-front to work itself out instead of going splat at the end of the can.
One thing to note for folks just getting into 5 series repairs, for the ignition coil reinstallation the gap is not like the older series of Husqvarna of .3mm, instead the 5 series utilize a .2mm air gap on the coil to flywheel. Husqvarna offers gauges for both, or if you have a Stihl .2mm gauge that will work as well.
Another thing is that once you get the knack of working on one size of the series, you can work on all, as the design is familiar throughout the entire family of saws.
Personally speaking, I find it unnecessary to remove the coil, especially after I went digital for timing, I just remove to flywheel, which has to come off anyways and use the timing apparatus to turn the engine over instead. I also leave the air injection duct installed as well as the front handle, the spring can be removed with the aid of a wrench for the attachment nut. That's a time saver I learned from having to change out springs from saws.
As far as the question to what the stand offs are for on the cylinder bolts, I can only say after repairing and working on quite a pile of well used saws that the benefit is all the wood-boogers and gunk does not settle in the top of the screws and difficult cleaning is not necessary prior to removing them with your T-handle.
The dished piston is not to be worried about unless building a GTG saw for racing, then an old-style Mark I piston can be exchanged. For a work saw this will go unnoticed and be beneficial overall to the saws health. I tighten up the squish a bit more than the Mark I to compensate some when doing the machine work.
Compared to older saws of the same displacement, the 5 series have smaller diameter pistons thus reducing the need for quad uppers. Also, the caps can be removed with a 20 torx security wrench and be ported without using a right-angle tool. Which gives the benefit of making the flow nice and neat on the approach prior to exit.