We commonly hear "A guitar is the sum of it's parts." To put that differently, they sound different because they ARE different. Forgive me if that sounds dismissive. It is not my intent.
It isn't uncommon for professional players to line up many of the same model and pick the one that sounds best (to them). I had two R9's that were 40 serial numbers apart. They were quite different.
Just because two guitars of the same model are made from the same type of wood, using same electronics, sporting same strings doesn't mean they'll sound identicle. You'd have to play a few with your baseline guitar present to try and make that happen. I'm guessing your two Siggy's sound close enough that most people couldn't tell them apart. But you, being intimately familiar with all of the nuances of each guitar, have educated ears. Educated ears can be a double-edged sword if you're not careful. I'm not suggesting we all go stick our head in the sand. Quite the contrary. I'm suggesting you put the issue into context.
My suggestion: Get to know them and apply their characteristics where they serve you best. Diversity on your tonal options is a good thing as far as I can tell.
I was once asked by a friend if I wanted to take classes with him to become a Sommelier. I thought about how much fun that would be. Then I realized I would only be shooting myself in the foot. I used to like $12 bottles of fruity red wine. These days it usually takes a $25+ bottle of "big" Syrah for me to like it enough to finish the glass (and that's without formal training). Since I am not serving wine to others for my income, becomming a sommelier would only serve to make it even more expensive for me to enjoy a glass of wine with my friends.
Hmmmm... Maybe ignorance IS bliss. Where's the sand?!
Lagniappe: Sniffing the cork is pointless. Doing so in a restaurant tells your waiter that you don't know anything about wine. Inspecting the cork is only good for checking that the wine was properly sealed and for verifying that the printed writing on the side of the cork matches the label. Scammers have been grabbing expensive (and empty) wine bottles from the trash bins of upscale restaurants, refilling them, and reselling them as the real deal. Source: Guitar Aficionado