Currently the MutationObserver cannot observe changes within a shadow-root unless explicitly set on the fragment. This is a problem for features like maintain.disabled where we observe changes on a context and filtered elements. As of right now any changed made to those shadow-roots will not be observed.
The purposed solution suggested by @rodneyrehm on #107 is to check for a shadow-root on all child elements of the context/filters and hookup an observer on all of the shadow-roots individually.