The simple way to understand this is to take a cynical view of the writing process.
The writer mechanistically removed synonyms from the work after completing it. Or got negative feedback about the wording.
So you can guess that what they originally wrote was something like
The modern world is different from ancestral conditions. It’s deeply mismatched in many ways.
It can’t mean because actually. The right hand side or second half is not an independent clause.
The ending—in many important ways—-is just a modifier. This is also true of ancestral human.
Then we can drop the modifiers and it should still make sense.
Dropping them and substituting because, we get
... we need to always keep in mind that the modern world is deeply mismatched because conditions.
The illogical result shows the initially assumed meaning, because, is not valid.
Ultimately in the context of the article that sentence means we have to remember that today is different from the past.