Ok, I found out what’s happening for me, at least. My problem was specifically with the allowed/excluded tags not being overidden.
On line 333 of Advanced Excerpt 0.2.2, you have this:
$allow_tags = $advancedexcerpt->array_complement($allow_tags, $exclude_tags);
But $advancedexcerpt->array_complement doesn’t return anything, so the allowed tags gets erased before the filter function is called.
Adding return $c;
to the end of that function fixed it for me.