Well, my experience is limited, but with my car(s) I've only rebuilt stock front control arms and I have used the ES bushings. I always attached the rear joints first and then swung it up to have the ball joint attach to the knuckle afterwards. That being said, I don't remember having to fool around much to get the 2 rear joints in place and bolted up. In fact, I'm quite certain I torqued the bolts to spec on the rear joint(s) prior to installing the knuckle so that I wouldn't have to do it with all that stuff in the way, and it all went together fine.

If you flip the bushing and everything lines up perfectly I'd run it like that, assuming you do some sanity checks and all the attachment points seem to be in the same approximate location. Seems like more of a bushing issue than a control arm issue, though that joint does seem to protrude slightly further out than the old one.