I empathize with the developer, but Occam's Razor suggests this isn't anything more than a typically crummy vague Walled Garden app store rejection. I'd take their advice and re-submit.
However the email I received is titled "Chrome Web Store: Removal notification for uBlock Origin".
In any case, it's just impossible for me to figure what is the issue. I could spend a inordinate amount of time guess-shuffling code around for no result.
Assuming the email title is misleading -- let's say uBlock Origin won't be removed from the Chrome store, there is nothing special in 1.3.2 compared to any other releases, and from the look of it I won't ever be able to fix whatever is deemed wrong without specifics, and as a consequence, no updates lead to abandonware.
Edit: I will add that with Firefox and Opera, there has always been communication with specifics when I was asked to fix something, and I always did fix as demanded (or suggested).
Have you tried telling them that?
Failing that -- if it were me -- I'd resubmit perhaps with the only addition of a README that briefly explains the file layout.
I’d caution against the shuffling code around to try to reverse engineer the approval rules. I tried the same with a similar extension (Adblock Fast) that got rejected for similar reasons (no reasons as far as I could tell). Result: my dev account got automatically suspended. I had to get a Google friend to get me unsuspended. Google seems to have added very aggressive automated approval and suspension rules. I’d reply to their email and see if they reply back first.
Updating them at first start would fit the description of not having them visible in the package.
This demonstrates the problem here, we are left to speculate endlessly about what the is the issue(s) according to the Chrome store.
This is the same thing that we chastise other people for. Yet here we are ready to switch to FireFox and Edge due to what is surely an automated misunderstanding. We are better than this. If not, we _should_ be better than this.