At least in Russia, "orthodox" has an extra connotation that's not strictly coupled to church, akin more to "one true way", as in "orthodox way to learn a tech stack". With a negation, it becomes something like "wrong" or even "heretical", as in "pizza with pineapple".

Replying to: Dual-pane file manager. For some reason, the technical term for these is Orthodox File Manager

The "orthodox" comes from a specific type of GUI, namely one that is driven by commands under the hood. UI elements are merely used to trigger commands that have the actual effect, and these commands could just as well be executed by hand, or automated into more complex commands. This is an excellent way to build powerful UIs. It is what drives things like Vim, and often why Lisp-based software is so hackable -- think Emacs, StumpWM, etc. Instead of writing plugins against some small plugin API, you're wiring new functionality directly into the application.