From someone who's lived in China and seen the supply chains for "fakes" and "authentic fakes", I have an idea about what this is.

For the differences in shape and size, looking at the MUJI site, they've definitely changed their design. The smaller tipped pens were their old design, but online the ones they're selling currently look like the ones you bought on Amazon.

As for the difference in quality:

For some unlicensed retailers, it's not worth it to produce their own "fakes". Even though the originals are so simple and minimalist, they have very specific details in their design and material that it's more difficult than you'd think to replicate. Small holes in the cap, even the length and depth of threading.

What they'll do instead is buy from "black market" sellers. These sellers usually obtain their goods through not-exactly-legal channels. Factory workers who pocketed some in the production line, workers at the shipping centers, etc. The most common form is buying products that didn't meet quality control in factories. This theft flies under the radar because these products were going to be gotten rid of anyway and aren't sellable. So no one's paying attention to their quantity or cares where they're going, so some people in the supply chain will take this as a "why not make a quick buck anyways" and sell these defective products for cheap to resellers, who will then sell them to customers pretending that they're "real". But they're really just "authentic fakes".

I'm not certain on this, but the Amazon MUJI store could be one of these resellers. MUJI has its own online store and the site has no mention of an Amazon store. This is just speculation but I'd say this is likely a Chinese reseller (most of them are China-based) taking advantage of China's terribly lacking copyright laws to pretend to be MUJI.

That's what I would say likely happened with these pens. They look very authentic to the smallest detail design-wise, but the worse quality you're likely feeling plus the sketchy retailer makes me suspicious. It's very hard to catch these resellers and regulate the supply chains.

Of course, I'm not in the business of selling fakes so take most of this with a grain of salt. I could be wrong. This is just what I've heard from living in China.

I did email MUJI to ask if the Amazon MUJI store is a licensed retailer, so I'll update in this subreddit when they respond.

EDIT: I just pulled up the Amazon MUJI store. I am now 100% sure that this is a fake reseller. If you look at this image, you can see the label "This product is from a small business". I'll bet my boots that this means that whoever set up this store wasn't affiliated with MUJI, the multinational corporation. Link to product - see if you can see it yourself.

That looks like a Muji Pen Muji USA or on Amazon Amazon Muji Pen