Custom Entity: define a view in entity reference field
The handler settings are part of the base field itself, rather than being a setting for the form display.

This should work:

$fields['user'] = BaseFieldDefinition::create('entity_reference')
  -&gt;setLabel(t('User account'))
  -&gt;setDescription(t('The user account this profile is connected to'))
  -&gt;setSetting('target_type','user')
  -&gt;setSetting('handler', 'views')
  -&gt;setSetting('handler_settings', [
    'view_name' =&gt; 'users_without_profile',
    'display_name' =&gt; 'entity_reference_1',
    'arguments' =&gt; [],
  ])
  ...