I have actually created two PHP modules, one is a contact form and one is a the "call now".
I can access the contact form by
example.com/contact_form/contact_form.php but in contrast,
example.com/call_now/call_now.php is of course something which is not a standalone webpage, rather just a caller for some HTML-CSS.
I can understand why you recommend to edit a skin's main PHP file; in theory I could paste all the PHP code currently in
call_now.php inside the skin's main PHP file but the problem with that is that it each time I would upgrade MediaWiki I would have to re-paste it there again.