SpriteKit's textures, texture packing and texture management have been fundamentally broken in iOS 9, and show no signs of being fixed anytime soon.
Right now there is probably no "best practice" that meets your requirements as I suspect the entire asset management and its procedures are in a state of flux. Perhaps they'll be fixed in iOS 10 in such a way that there's an ideal, but given the debacle that is iOS 9 and Sprite Kit, I doubt it.
If you're not aware of this thread, a read through will give you some idea of the problems:
https://forums.developer.apple.com/thread/17463
This one also an interesting read:
https://forums.developer.apple.com/thread/14487
The above are indicative of the more general problems with Sprite Kit in iOS 9, and should give you a feel for how immature or otherwise wonky the thing is, as a whole.
More pertinent to your question, things like this go unanswered:
https://forums.developer.apple.com/thread/26059
If your question is:
What are the best practices for an asset-heavy 2D game with lots and
lots of sprites in SpriteKit for keeping final binary size small?
And we ignore "SpriteKit" in this question, the answers are vastly superior than any option currently available within SpriteKit.
Unfortunately Apple seems to have gone to enormous trouble to promote, posit and claim its game engine technologies as appropriate for asset heavy productions, despite concurrently claiming them to be easy to use and good for casual game development, and getting neither claim to hold up to any scrutiny.
For a brief period towards the end of iOS 8, most of Sprite Kit worked as advertised, but that all changed with iOS 9. Now its texture handling has reverted to the problems prevalent in iOS 7, and some new issues, too.
The Apple forums document significant other problems, and varied performance issues within iOS 9's Sprite Kit, too.
Yet there is no word from Apple that acknowledges these problems, let alone addresses them.
It is wrong to recommend Apple's gaming technologies in their current state. A lack of meaningful criticism of Apple and their game technologies doesn't mean these things are without show-stopping flaws.
Until they really knuckle down and get a product manager focused on their game technologies and release things when they work, I'd say cocos2D-X and one of the commercial texture packers is the best practice for your requirements.