Well, you're right. The "nude" mod the K1000 to sit flush on your earlobes, no space in between.
As a consequence, the spatial presentation does change from "normal" K1000 mode. When K1000 is used normally, adjusted to give the best spatial presentation (usually sitting quite a bit away from the ears), I felt the tonal balance, detail retrieval, bass was not to my satisfaction. I still preferred it as close to possible to my ears, which I felt gave better tonality and bass without sacrificing the soundstage too much.
The "nude" mod takes it further. The tone is now "correct" IMO with much more dense/richer lower midrange/upper bass/mid-bass balance. Bass is unbelievably improved in quantity and quality. But the entire frequency range is better detailed and clearer at the same time, likely due to less distortion b/c the driver has to move less to produce same perceived volume.
Even with the "nude" mod, the sides of the K1000 are open, and you do get cross-feed from the other side. I really do not feel I get a less spatial presentation at all. If I want a soundstage like speakers, well I use my speakers. You do realize that I used to use K1000 in "normal" mode for a long time before the nude mod. I do not miss the normal mode AT ALL, spatial or otherwise, and I will never go back since I now know what K1000 is really capable of in terms of musical satisfaction.
As far as comfort, the nude mod is an order of magnitude more comfortable than the Grado HP-2 or Sennheiser 580. It's much lighter without the headband, and the wire over top of head carries most of the (light) weight, and the earspeakers can gently sit on top of your ears with adjustable pressure.