because they are COMPLETELY different animals

if you want to filter things in the non-standard templates, have a look inside
inc/markup.order.html.inc.php
and use the filters in there

perhaps – for simplicities sake the one near the end named
wppizza_filter_template_html_message_markup

but it depends what you want to do, there are other filters in there too.
possibly the ones marked with

/**allow filtering – unused in plugin**/

>1. Should i edit the inc/markup.order.html.inc.php if I want changes in a custom mail template?

NO, NEVER EVER edit core files. the ONLY files editable are the ones in /templates/ and even those should be copied to your theme directory if you want to edit them directly.

the filters added in that file are to be used as such . i.e as filters in your theme’s functions.php (like any other wordpress filter and/or action hook)

if you do not know how to use wordpress filters , please learn about how these work.
plenty of resources on google the explain this better than i could ever do

other than that , i might be able to add some example here, but a busy with a number things, so will take a few days