I was really hoping once you posted pics someone might chime in and give more insight!
From what I can see your mare has a straight shoulder, so her shoulder blade(tips, where your saddle tree would interfere) when moving probably has a more up and and down movement rather than a forward and back movement that would see on a horse with a sloping, less steep angled shoulder. Also from looking at your saddle pad it is hard for me too say, but those dark round spots behind where the white is on the shoulder part is what might worry me, are those spots where the pad is not making contact or is it pressure spots? What does her sweat marks on her back look like? Dried out or hair roughed up compared to the rest of the sweat mark?
(one thing for sure the skirt style or length doesn't seem to be an issue.)
I DON'T LEAD 'EM AND FEED 'EM, I RIDE 'EM AND SLIDE 'EM.