Definitely align the metal with the end rake. That way your end cap will run even with it. If the metal is running out of square to the eave, you'll be best to measure the shortest side of each sheet off the fascia for proper overhang. Chalk line, and trim even however you decide. I prefer 1-1/2". On my two new buildings, the design guy and contractor assured me 3/4" would be enough, even though I pretty well wanted the 1-1/2". WRONG... In a misty drizzle, or even a heavy morning dew dripping off, it will wick back, missing the drip edge, run down the fascia, and behind the gutter and now have a drip line the full length of the buildings.
One half of the shop roof leaked after 8 months, due to them putting screws in the flat of the metal, per the metal companies directions, not mine. Had them take that off, and re-install a new roof on that side of the shop, and insisted on a 1-1/2" overhang. Problem solved on that one side. The rest I will have to live with, or put a piece of flashing to get the water out further over the gutter.
And as far as the fascia running in and out, seems some contractors set the trusses measuring off the header, but don't follow through and strike a line with a chalk line end to end on the rafters, and cut to even it up all the way through, as I was taught many years ago.