Even when I was in much better shape and very flexible I have never been able to sit like that. My ankles were never ok with it. I have also oddly never been comfortable on my knees.
You have to pull your hips in, that allows your rear end to touch your feet without pressure and you hold a lot of the weight in the core, so there isn't all your weight either pressing on your toes or pressing on your knees. You need a certain amount of flexibility in the hips, hamstrings and outer thigh muscles. If you don't do that you'll end up in kinda Z shape which is where the pain comes from.
That can help, sure. Learn to sit for a few minutes each day in seiza while you're watching TV or stretching your arms, or whatever. Try to remember that Japanese people adopt that posture from a young age because of their culture but that doesn't make it ergonomically ideal. It's too much pressure and weight on critical walking joints without a lot of advanced flexibility and proper instruction beforehand, especially if you're kneeling down on a hardwood floor of some sort. As an MAist, your knees are eventually gonna go out on you. Kneeling on them unnecessarily will only speed that decline.