Python is (unlike java rustc, node etc.) preinstalled on every Linux Distro out there, so Programs are coded with that in mind, that they always have access to Python. Python belongs to any Linux runtime.
The Meson buildsystem (which is supported by flatpak-builder out of the box) is written in Python, so it would not work without Python being installed.
There are also a lot of build scripts written in Python.
The backside of this is, that a new Freedesktop SDK is releases each year in August, while a new major Python version is released each year in October. That means, that you have to wait a year to use the newest Python features or compile Python from source.