From the docu:
”
Many newer event options are stored in properties, see eme_events.php function eme_init_event_props(), for a whole list.
A small enumeration:
auto_approve (*)
ignore_pending (*)
all_day (*)
take_attendance (*)
min_allowed
max_allowed
rsvp_end_target
rsvp_discount
rsvp_discountgroup
use_worldpay (*)
use_stripe (*)
use_braintree (*)
use_stripe (*)
”

In your case: the property you’re looking for is “person_only_once” or “email_only_once” (see eme_events.php function eme_init_event_props(), for a whole list).

No, *never* change the code. That is not what the doc says. But for changing it “by default” (so without asking for it), use the EME filter eme_event_preinsert_filter for this.
The next version of EME will have eme_insert_event_filter (a bit more logical name).
I also created such a filter only for EMEFS (in the version released today): emefs_event_insert_filter

This should do it:

  function my_emefs_event_insert_filter($event){
      $event['event_properties']['person_only_once'] = 1;
      return $event;
  }
  add_filter('emefs_event_insert_filter','my_emefs_event_insert_filter');