There are no hooks in wpautop(), at all. Given that this is possibly the most complained about function in the WordPress world, it is odd that there are none but there you go.
What you will need to do is remove the filter:
remove_filter( 'the_content', 'wpautop' );
remove_filter( 'the_excerpt', 'wpautop' );
Create a version that does what you want, and add that filter to the same hooks:
add_filter( 'the_content', 'my_wpautop' );
add_filter( 'the_excerpt', 'my_wpautop' );
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