FEP doesn't conflict with complex dynamics, it's a mathematical framework for explaining how self-organizing behavior arises from simpler variational principles. That's what makes it a theory rather than a label.
The thing you're doing here has a name: using "emergence" as a semantic stopsign. "The system is complex, therefore emergence, therefore we can't really say" feels like it's adding something, but try removing the word and see if the sentence loses information.
"Neurons are complex and might exhibit chaotic behavior" - okay, and? What next? That's the phenomenon to be explained, not an explanation.
This was articulated pretty well 18 years ago [0].
[0]: https://www.lesswrong.com/posts/8QzZKw9WHRxjR4948/the-futili...
