Removing the rear foam will bring out the mid-bass. Adding damping behind the driver will help lower it, and bring up the treble a bit, at the expense of making them sound even further overdamped to the point where they might develop a sort of high-pitched grain or sense of strain to them.
Perhaps removing the foam directly behind the driver but adding foam within the cups could be a way to dial in the bass without overdamping them as much. I haven't tried it.
The foam in front of the driver also plays a role in the amount of mid-bass. Remove it entirely, and you lose a lot of bass...and get some nasty treble effects. If you cut a larger hole in the front foam than the mod suggests, so you can see more of the surrounding silver material around the driver, you may get some positive benefits to your ears.
Personally, I like the mod as-is, even with the extra mid-bass. Pair them with an amp that doesn't add too much thickness to the sound, and it balances itself out nicely. The modded HD650 pairs very nicely with the Valhalla 2 and NOS Telefunken tubes. Val2 isn't particularly thick or bassy sounding, nor are those Tele tubes. Works great with the modded HD650.
Could also try some enclosure/frame damping to see if that reigns in the bass.