Cannot use regular Jupytext markdown notebooks

[choldgraf]

In executablebooks/meta#272 (comment) @parmentelat noted that it wasn't possible to use non-MyST markdown notebooks from Jupytext. For example, the following configuration:

nb_custom_formats = {
    ".md": ["jupytext.reads", {"fmt": "markdown"}],
}

raises this error:

Extension error:
source_suffix '.md' is already registered

[juhuebner]

Would it be possible to opt-out the registration of the default suffixes here if needed, since it is easy to get them into the sphinx config but hard out again?