There is generally no way for the average consumer to differentiate between a design issue and a manufacturing issue. Of course it doesn't necessarily matter to some extent, but often times (not always!) a manufacturing issue is likely to effect a smaller portion of a production run.
And considering this isn't common to other Fujifilm cameras, I'm thinking that is likely to be the latter case.
So I voted with my wallet and bought an X-Pro3 a few months ago.
I also rationalize it this way - one of my all-time favorite cameras ever made is the Ricoh GR. And you can't find a forum or review that doesn't mention dust on the sensor.
And yet I have owned 3 different bodies: a GRii and then two GRiii's (one was stolen), and I have have carried them everywhere: rock climbing, motorcyle trips, to the beach, every where, every day and guess what - no dust.
So in the end I just buy what I want to use and don't worry about anything else.
Edit: I would only add that I'm not trying to be dismissive of people who have had issues, I totally get that. It's just that for me, I've weighed the pro's and con's and I'm willing to take the risk in order to use the tools I want to use.