functions.php will load automatically for every page load, but you could certainly move most of the content of your current functions.php to other files and use functions.php itself as a primarily a kind of switch.
Caveat: You may have to hook some of your switching functions to get access to certain data. For example, functions.php executes before the main query (which is why the pre_get_post hook works if called from there) so things dependent on the main query won’t be set correctly in functions.php.
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