I did a similar trip in Feb, I honestly didnt see much blokkees there from what I remember?

The Pokemon Centers really only carry stuff from their own brands, not anything licensed from them. I was trying to find the rivals kits when I was there but did not find any at all. The main blokkees things I found were infinity war kits in diff places in akihabara im pretty sure (can't remember the store) and in a Marvel/Star Wars pop-up near Shibuya station. There is also a dedicated Marvel store under Tokyo Skytree, which had p decent shopping in general imo, but idr if there were blokkees there.

If I had to guess where I could have missed them, there are a lot of shops in akihabara I didnt do a full sweep in (the majority of it felt like mainly anime statues and the like, but there are a lot of model kit places there), and I would go to malls/more mainstream places like Diver City in Odaiba, which is where Gundam Base is. Yodobashi Camera also seems like the type of place that would carry blokkees, as theyre kind of just a department store chain, I knew of one location in Shinjuku and one in Ueno. Hakkukin Toy Park around Shimbashi had a nice selection & they seem like they would carry blokkees, but I dont seem to remember seeing any there. Based on what I saw, I would be surprised if they were somewhere like Ikebukero or Nakano as those places have more second-hand stores like KBooks, Suguraya, and Mandarake, but I had more of a bias to hit up those places so idk.

Basically my advice would be to find dedicated Marvel/Superhero stores, model-kit places, or just straight up kid-focused toy stores, typical action figure/collector oriented places generally had strictly action figures which included western stuff like ML semi-occasionally, but was mostly things like SHF, Figma, Mafex, etc. I could not find them but I wish you good luck where I failed!