I dont think it is uncomfortable at all. It does take some getting used to and some practice. I started out working on my seiza some 25 years ago. I started by sitting seiza 2 minutes, then increased to 5. Every couple of weeks I would add on time spent sitting in seiza. Gradually I built it up to 20 minutes. Sometimes I would only do this for the set time. If I had more time I would sit down for my two minutes or ten minutes however long I was sitting seiza for then I would stand up stretch my legs walk around a bit and sit back down for another 2 minutes or 15 minutes or whatever the time that it was. Other times I would sit seiza during the tv commercials. When the show started again I would sit back up on the couch or stay on the floor. I like being on the floor anyways, kind of closer to earth. Then after a while I started watching tv in seiza, and occaisonnaly eating in seiza at the coffee table. I’ve also had some long winded sensei, so there was some extra seiza built in. Now granted that was in my younger days and I don’t do all that seiza training now, but I have no trouble sitting seiza for extended periods.
Now something you can do is shift weight to one side, let pressure off the other side for a minute or two, then shift to the other side. Another thing you can do is rise up to your knees and let the blood flow back into your feet. When I do this I will straighten out any clothes…gi, hakama..that have bunched up behind my knees.
Now after a while of sitting in seiza you will get the prickley needles feeling in your feet and they will go numb. Even though you can’t feel your feet in this case, they are still there, and the bones and muscles will work just fine when you rise, step, run and so on. The feeling will come back in a few minutes.