Muji definitely charges way more outside of Japan, ditto for Daiso. They did this when the Yen was in the range of 70-80 to the dollar, and they kept the premium when the Yen went weak to 125. Pocketing extra profit is good for them evidently.
I travel to Japan regularly so I just avoid buying Muji outside of Japan. Most folks probably don't have this option.
As to Uniqlo, the challenge is that not many stores in Japan carry western sizes. The only reliable store I have found in Tokyo that does is their main store in Ginza -- and even then, not too many items.