Q: FileBot is highlighting episodes in shades of red colour. What does this mean?

The red highlight colour suggests a possible mismatch. Stronger red means more likely to be a mismatch. Lighter red means less likely to be a mismatch.

The stronger red S06E01 match is actually a mismatch. The red colour correctly highlights the incorrect match here. You can use
Edit Match to manually fix the match.

The matches that are white
(i.e. not marked as possible mismatch) because the episode title in the file name matches exactly the episode title in the matched episode.