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Depends on where you ordered from. I got a 6S+ 16 GB about two weeks ago at the Apple Store (in Albuquerque NM, while I was there for the weekend). It had 9.0.2. Sadly, I found I needed more space, so ended up returning it, and got a 64GB from a seller on Swappa, but it turned out the device had no warranty, so I ended up returning it (no warranty meant any repairs would cost me, or whatever).

Got a 64GB AT&T 6+ yesterday at Best Buy and it had 9.1 - got home, jail broke it, and it went into a boot loop. Tried for hours, and various methods to get it out, with zero luck. So -- the ones with older versions of iOS are out there, its just a matter of what size/color and carrier you ordered, and from where.
 
Ordered from sprint. Space gray 128gb. They said it was not a popular option and it wasn't in the warehouse where I'm located, so they had to go to another warehouse in another state to retrieve it.
 
even if its on 9.1 i dun think jb will be available anytime soon.
 
I just got a new 128gb 6s from the Apple Store a week ago and it was running 9.0.2. Now it's jail broken and I'm a happy camper.
 
Ordered from sprint. Space gray 128gb. They said it was not a popular option and it wasn't in the warehouse where I'm located, so they had to go to another warehouse in another state to retrieve it.
If that is the case, you have a good chance it will be on a version you can jailbreak.

Higher capacity models sell less so the stock moves less. Which means they sit longer and therefore you are more likely to get a model with a lower version of iOS.

I bought my wife a 64GB iPhone 5 a year after the release of the iPhone 5. 64GB was the max capacity of that model so she got a jailbreakable version of iOS because it had sat on Apple's stockroom shelf for six months before I bought it.
 
I got a 128gb 6s plus replacement from apple yesterday and it came with 9.0.2. Needless to say it was jail broken within the hour
 
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