DannyA, I'm sure the guitar is fine and Rev may be correct in saying it won't harm the guitar. My buddy bought an Epi Wildcat a few years back and that was my 1st experience with a Bigsby. It was a cool playing guitar. The only problem was it didn't stay in tune after a few whammys and I suspect it's because it lacks a roller saddle bridge. I also noticed that his case didn't close all the way when he put the guitar away as he left the bar forward in line with the strings. In his case [double meaning], if he turned the Bigsby to the rear, the case would close so I suggested it would be a better way to store the guitar as there would be no string or neck tension released. He didn't care either way, but I thought maybe it's just me? Then a few years later I buy a Taylor T3 with Bigsby and low and behold there in the rear of the case is a notch so that the Bar can be turned all the way to the rear and the case closes all the way before latching...and the roller saddle bridge keeps the strings from hanging up and it stays in tune.
Long story short, it looks like Taylor agrees with me. If you move the bar forward in line with the strings, you'll notice the case is higher with the lid resting on the bar before closing. As you move the bar towards the rear, you'll notice the lid gets closer to closing and thus it pushes less on the bar when you latch the case. In your pictures, it looks like the best spot is right in the corner of the case, as shown in the 3rd and 4th picture and it keeps most of the lid pressure off of the bar.
My other buddy had a Bigsby installed on his Epi 335 (along with those 57 Gibson Humbuckers) but the bar stuck up too high, so he bought a replacement spring with less height and removed the spacer (as opposed to having the bar bent in a vice). Now the bar is lower and feels better and his case closes. He also installed a roller saddle bridge and it stays in tune. He also has a T3 and sees the way the case notch, Bigsby and roller bridge all make some cool improvements. Next time you're at a GC, pretend you're interested in a guitar or 2 with a Bigsby and see if the case closes, you might find that it's no big deal and they all close that way or you might find a better case...have fun!
ps. I noticed your Bigsby roller where the string ball ends connect is mounted at the rear of the guitar body with no plate, my T3 has a plate like the one shown on Sockfoots' Ibby and more guitar body (about 4") between that roller and the end of the body, which allows the bar to stick out less passed the body when turned all the way to the rear.
pss. It would be cool if Bigsby would grind off most of that bar stop as Scott describes and maybe even come up with a quick disconnect removable bar for the no-base plate models...