You should be able to hook into the admin footer and add in any kind of datepicker option as you need by field ID:
/**
* Modify ACF Datepicker Formatted Field
*
* @return void
*/
function theme_prefix_admin_footer() {
?>
<script>
jQuery( document ).ready( function( $ ) {
let $datepicker = $( '#acf-field_5b16a9d5df47c + .hasDatepicker' );
$datepicker.datepicker( 'option', {
altFormat: 'dd. M yy'
} );
} );
</script>
<?php
}
add_action( 'admin_footer', 'theme_prefix_admin_footer' );