In the internal docs is explained why the extension is written as it is. https://internals.phalcon.io/en/latest/
In addition, we created the Phalcon Kernel (https://github.com/phalcon/cphalcon/tree/1.1.0/ext/kernel) which is a super API allowing us to write C code following a similar philosophy/workflow as PHP, this helps developers to understand better how the extension currently works, a developer can contribute code to phalcon by just thinking in PHP.
Some critical parts in terms of performance as some parts of the database access, the parsers, volt, phql, are written without using Phalcon Kernel.