1

I'm looking to follow this other answer regarding linting inside org-mode source code block but I'm not able to figure out how to tell flymake to disable certain backends.

I'm using Emacs 27.x

2

See flymake-diagnostic-functions:

The functions in this hook diagnose problems in a buffer’s contents and provide information to the Flymake user interface about where and how to annotate problems diagnosed in a buffer.

Just remove function that you don't need like this:

(remove-hook 'flymake-diagnostic-functions 'flymake-function-that-you-dont-need)

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