>>9790539Pretty much what
>>9790547 says. My personal theory is that Bulkhead was one of the first toys designed for the line, before the "multiverse" gimmick was decided on (hence why Prime is the only continuity to be redesigned), and back when they didn't know how well Micromasters were going to sell.
But Bulkhead was designed to make use of the Minicon gimmick, and it was too late to remove the ports. So when Micromasters failed and were cancelled in Kingdom, the Minicon gimmick was removed from Legacy. Needing a new gimmick, they decided on the OTHER gimmick from the Unicron Trilogy, Energon weapons. So they shat out some Energon weapons, except they required using the same clear plastic sprues as the rest of the toy, to save on costs. Since most toys didn't use neon-colored clear plastic, they had to use whatever they DID have, which in most cases was either *no* clear plastic, or smoky grey clear plastic, to resemble windshields.
tl;dr: Bulkhead has Minicon ports because Legacy was going to have Minicons, but when Micromasters failed they needed a new gimmick. They settled on Energon weapons, but had to make do with whatever clear plastic they had lying around.