...understood by/through studying its

When the meaning involves "obtaining" something, both "by" and "through" are generally correct and understandable -- and other prepositions can work as well.

"I gained knowledge (by/through/from) studying x"

"I earned a good living (by/through/from/when/while) working in the financial industry."

In the case of "learning something," then "through" might suggest more time or more of a process than "by," but both clearly point to a source of an outcome. I don't believe there is a best or more correct choice between "through" and "by" in the example given.

Idiomatic usage may be hard to predict, and idioms are by definition irregular in some way/s. Prepositional usage can often be deemed to involve idiom.

I'd choose understood by studying or understood through the study of , and I'm gratified to see that Google ngrams don't contraindicate.