They are two different games with two different lobbies with two different sets of players (although admittedly there is overlap).

If it's not possible to separate Halo from Custom edition, could a filter be implemented on the search to only show Halo servers or only show Custom Edition servers?

Edit: NVM I think this is actually not possible since Halo Servers and Custom Edition servers seem to have the same server variables (e.g. you can't differentiate between them).