FileBot

Make a directory named 'Gunbuster' and inside create a file called 'Gunbuster.05.Chapter.04+1.mkv'. On that file, run the following:

('episode.special >= 1' is so it's limited to special episodes)
It should incorrectly name it 'Gunbuster - 0x04 & 0x05 - Science Course - Chapter 4 The Size of the Fiendish Space Monsters & Science Course - Chapter 4+1 The History of Spaceships.mkv' when it should be 'Gunbuster - 0x05 - Science Course - Chapter 4+1 The History of Spaceships.mkv'

Is it possible to force FileBot to interpret each file as one episode?

You could do --filter 'episode.special == 5' so it'll only consider Special 5 for matching. You'd need to change the filter for each special episode though so it's not a good solution.

EDIT:

Fixed with r4646.