WordPress uses those markers to put its rules between. I never have and never would put custom rules in there.
Check out insert_with_markers()
and save_mod_rewrite_rules()
in
wp-admin/includes/misc.php
Most notably this comment block which answers your question:
/**
* Inserts an array of strings into a file (.htaccess ), placing it between
* BEGIN and END markers.
*
* Replaces existing marked info. Retains surrounding
* data. Creates file if none exists.
*/