VicBC_Biker gave some good pics that sort of show what I was trying to say. See how the DR is stretched out in the big's, but has clearance to the jockey wheel. My 105 5800 GS (mid cage) DR looks stretched out like that too when in the 52F/32R. While a lot of literature might make you think that is too stretched out, as long as you have the clearance to the jockey wheel and the DR isn't at it's limit to stretch out more, then you probably are okay.
And clearly when in the smalls the chain isn't hanging slack with a big curve in it.
As for your bike, you ought to have it right side up when you adjust shifting and DR's. Gravity does have some effect on the components that will be different when you turn it over. You can just hang your top tube over the corner of a table or clamp some 2x4's through a ladder to hang the top tube on. Sometimes I just hang the nose of the saddle on something.