Ref T4379. Fixes T4359. Currently, bin/search index does not rebuild CustomField indexes. This is because they aren't really part of the main search index. However, from a user's point of view this is by far the most logical place to look for index rebuilds, and it's straightforward for us to write into this secondary store.
At some point, it might be nice to let you specify fields as "fulltext" too, although no one has asked for that yet. We could then dump the text of those fields into the fulltext index. Ref T418.