I did a further test with different Matrix Installation (3.28.1) and adding/deleting design customization.
If you create the design customization after the design files (css, js, images, favicon etc) then it doesn't create extra URL path to these files.
But if you create any new assets after the customization had been created then it gives extra URL path's depending on the number of customization you have. So for example if you had 3 then all your new assets inside the design file end up with 4 URL path (1 original URL / 3 design URL path).
I strongly believe this is a BUG that was created after 3.18 because we had 10 design customization in one design file and files created after these design customization didn't get extra URL path's. We recently got upgraded to 3.28.3 and now it gives 11 different URLs to any new asset that is created in the design file.
I'm not so sure this is a bug. It looks like there is a webpath for every link, so there might be an explanation for this. Is this a Squiz-supported system? If so, I'd recommend emailing support@squiz.co.uk and getting somebody in the team to check it out.