Don't work with custom field handler

We use hook_entity_base_field_info_alter() and hook_entity_bundle_field_info_alter() to alter a entity_reference field's handle, so that we can restrict the selection results.

$fields['field_store']->setSetting('handler', 'custom:group_commerce_store');

But it don't take effect after change field's form widget to select2boxes_autocomplete_multi

These days we give up custom EntityReferenceSelection and use custom Entity Reference views filter instead.
Like this:

When we change to Select2 boxes (Multiple values), Everything works fine ,
But After we enable pre-loaded entries,The Entity Reference views filter lose efficacy