Those weren't left-over bodies. Gibson did not have an inventory left over when they switched to the SG-style.
But when they decided to reissue the LP in 1968, they were basically clueless about which version of the LP people wanted. These were the early Norlin years, Ted McCarty had left a couple of years earlier, and Maurice Berlin had been moved into a meaningless job. Management, in short, was in the same position as CBS when they bought Fender: full of hubris but way short of any knowledge of guitars or the market.
So they offered two LPs: the Custom, with full-size pickups, and the Deluxe, with P-90s. When the dealers clamored for a humbucker standard, Norlin looked for a cheap fix and Jim Deurloo discovered that the Epi mini-humbuckers would fit in the P90 rout. It took a while to get the tooling right, and a lot of the early ones (including mine) have creme plastic "goof hiders" around the pickups to hide tooling marks.
This led to other anomalies (the peculiar mounting system for the minis, for example) and did not quiet the true believers, who were paying big bucks for the "real" thing -- the full size humbucker. As Milnoque noted, the minis have a sound of their own. A Deluxe is the only LP I've ever owned, or expect to own, because to my ear they are greatly superior to the full-size model.
Which didn't stop me from recently trading for an Epi Sheraton II and ordering a set of Seymour Duncans for it. Dispassionate research will follow.