You sure you have the version number correct there?
Multi-episode files are fine, but they need to be in the same season. You’ll need to split the file or unmonitor one of the episodes for Sonarr to not report it as missing.
That depends on the indexer being able to return the results if Sonarr searches for either that season or one of the episodes in the multi-episode file. Proper indexers that allow search by ID, season and episode shouldn’t have any issues, but others might.
So, not fine since this is a multi-episode file that covers the end of season 3 and the start of season 4. There is no question this is a two parter, and it does span the season, so not handling it properly is a bug that should be addressed.
I have no problem manually searching the indexer for episodes that Sonarr claims there are no matches for (for example, it found no matches for TNG S04E01, S07E26, or any other multi-part episode in TNG’;s run.)