I believe there was a bug when if you didn't populate certain banks you could circumvent certain weapon limitations. For example, if you didn't populate the second primary bank (with 6 gunpoints) in BP's Uriel, the contents of the third bank were moved up by the amount of empty banks, resulting in this case in you having the Archer in your 6-gun bank, which is not allowed there.
So someone came up with the idea that in order to not make this happen (and to prevent the need for diving into complicated and poorly documented code), it's just needed to never let a fighter have an empty bank. Then it turned out that having empty banks would be really useful in some rare circumstances, like yours, and that actually at least one retail mission loadout has empty banks.
Though I'm not sure what SCP will decide to do with this.