There’s an excellent free tool called Renamer you can use to change your image names in batch and solve the problem.
You could drop your entire music folder into it, choose the “replace” option and set the name your jpgs use as the string to find and change them all to something like “coverart.jpg”.
Problem solved in less than thirty seconds 
I don’t want external covers. Thankyou though.
No worries, it would just stop any of those random cover.jpgs you said you had strewn across folders from being a problem. But if you don’t want them at all, make the string just the .jpg file extension and this will tell you what folders they are all hiding in 
Ah I get your point. Thankfully search on both windows explorer and mixplorer searches worked fine