Multiple event lists

Yes, you can use two separate events_list shortcodes, each with the attributes and formatting you want that particular list.

This should help:
https://wp-events-plugin.com/documentation/shortcodes/

Can I use the shortcodes in PHP using the echo EM_Events::output($args)

That should work fine, you can also use the WordPress do_shortcode function too:

https://developer.www.ads-software.com/reference/functions/do_shortcode/

Thank you caimin_nwl.