What could be causing these short internodes?

It could be those mites that also cause witch brooming in pines.
Those mites attack buds in late summer, and they're basically invisible critters (as small or smaller than spider mites) and they leave no trace. But the plants response is out of this world in the sense that the mites do a better job at producing bud proliferation than almost any plant hormone can.

High cytokinin vs. auxin content explains all that we're seeing here.
Can these mites be "weaponized" for bonsai purposes?
 
Can these mites be "weaponized" for bonsai purposes?
Probably, yes. But that would take some work of proper ento.. entomotologists? Whatever they're called: Insect scientists!
Scientific literature is super sparse about them and most descriptions are closer to anecdotal than they are scientific. I hope some young person comes along and thinks "Heck yeah, I'll go ahead and make it my master thesis research!"
But if you get sudden witch brooming on a pine, please do rub other buds on those brooms to see if you can pass it on. However, the congestion of buds is usually very difficult to provide sap to and a lot of them will die due to sap flow issues.
 
Can these mites be "weaponized" for bonsai purposes?
Not really, I purchased a scots pine for fairly cheap that has some mite issues and those branches are kinda jacked up and will likely need to be removed. I'd rather have a healthy tree.

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I did get flat mites on my Portulacaria afra and it basically turned them into corkbark P. afra. After treating them the plants were fine.
 
Here are some pics of one of the four rubrums I have. Set this tree back pretty far with last year's mistakes on it. Time and patience.....
 

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What is this, internodes for ants?!?
 
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