1.Trim the seat (no impact on suspension but probably get a sore butt because of the soft seat foam)
Not necessarily so as evidenced by the fact that several members have done this and have not reported any cases of sore butt. Of course, that could be relative to one's butt sensitivity. Shaving MC seats has been done extensively for a long time with many brands.
2. Reverse the eccentric (less cornering clearance and larger rake angle)
I am not aware of anyone ever advocating dropping the bike at the rear, and then not matching the drop at the front. Speaking for myself, I always try to stress that the front needs to be lowered the same amount as the rear to restore the factory configuration. However I do wonder just how significant this is because I suspect there are a multitude of MC riders of all marques that take a pillion rider with no concern for the change of bike geometry?
As far as boot dragging goes, keep the balls of your feet on the pegs, and tuck the inner boot in tight when cornering. That should be the first step of your cornering set up. I know for a fact that this works on my lowered ST.
Some have expressed concern re parts scrapping. The first time I scraped the feelers, I stopped and removed them. Maybe someone knows a justification for them, but I found them unnecessary quite some time ago. If you are just riding around town, and insist on carrying that hunk of metal called a center stand with you at all times, it should not be a problem. If you do track days, it should be removed.
My ramblings on this subject are not something that I read in a book, a magazine, or heaven forbid, on the internet. It comes from actually riding a lowered Sprint. As evidence you can examine my rear tire and make your own determination. I know that some dislike tire pics, but they are definitive and do tell the tale. No part of my lowered ST scraped with the exception of the ends of the pegs....a non-event. I have been unable to get rid of the front strip but that was not because of a ground clearance concern, just my personal inability......code words for 'fear'.