As far as I know, there never was a double muff in nonfootswitch boxes. There were two versions of the original muff fuzz, as you said, IC and transistor. The double muff is essentially, 2 muff fuzzes in series. The few extra parts, I assume, help shape the circuit, provide filtering, etc. It was discontinued a few years back, but EHX re-released both the muff fuzz (overdrive), and double muff with their xo packages.
I've been messing with a literal 2 muff fuzzes in one type double muff on the breadboard. It's a fun one.
Here's the guts of the two different DMuffs I mentioned. Obvious thing you'll notice is the layout...then the use of 5088's vs bc550's...the switch pcb...I think the values are the same. The right one is mine, and it use to have another cap+res in between the black leads from switch and board.