I agree, some cushioning is vitally important. As I prefer to be barefooted and my floor has no carpet or padding whatsoever my heels started to hurt at the end of the very first day. On the next day I felt that pain from the very beginning, so being productive was out of the question. Contrary to the general consensus I got myself a really cheap gymnastics mat for less than 20EUR which is only 2cm thick, instead of an expensive special purpose mat. Within 2 days the pain was gone and standing/working for more than 10hrs a day was not a problem anymore. So get a mat or wear shoes if you plan on trying a standing desk configuration.

Padding can dampen impact from jumping, but it cannot actually reduce the gravitational forces when you are standing. So I am very wary of this concept- instead, if you feel pain stop doing it. Padding stops you from using your feet and moves more of the stabilizing burden elsewhere, which could be bad for some people- although seems to be working fine in your case. Either way one is loosing out on the chance to gradually strengthen the feet in a natural way.

I can't upvote this enough. A proper mat made all the difference for me. I'd say it easily quadrupled the amount of time I could deal with working while standing and eliminated most of my initial foot pain.