I'm not saying we should remove copyright laws entirely, but it certainly can be improved in a lot of areas, because the way the world works has changed considerably since the first laws were written. If someone puts a Coca Cola decal on their car in GT Sport, are they a criminal because they have cost the company billions of dollars? I don't think so. In fact it's probably free advertising. You could argue PD has gained sales because of the livery editor, but how do you quantify this and distribute the revenue among every company that has their decal uploaded in the game? The complications goes on and on.
I'm all for people and companies protecting their IP (and getting rewarded for inventing something), but at the same time, it's common sense when someone is using it for non-malicious and non-profit intent and it should fall under "fair use". Selling a sweet carbonated drink in red cans and branding it "Coco Colo" > copyright infringement. Putting decals on a virtual car for a game > no biggie. Then you have the moral and ethical dilemmas with drug companies "evergreening" patents just so they can have monopoly on a life saving treatment for longer. Is that correct use of copyright? Legally and financially of course, but looking at the bigger picture, it's debatable.
Then again, I'm not a lawyer, and I haven't made anything worth copyrighting, so what do I know?
If any company was to take issue with people using their logo in a game their primary concern is likely to be what it is associated with/misrepresentation. Not saying you have of course, but a livery with a Coca-Cola logo on one side and a swastika on the other side could cause obvious problems when it's plastered all over the media, where it wouldn't matter to most people that it was user created. Well, you know what the media is like these days, it would purposely not be mentioned by a large part of it. You can see why a company would want to avoid that.
Then on the misrepresentation side you actually covered in the other direction, so imagine someone places the logo for an ethical human rights charity and alongside it they place the Kit-Kat logo/design, just because it looks nice or whatever. Now again, someone sees that and suggests the human rights charity are supporting "Water isn't a right" Nestle. The charity aren't going to want that.
One further reason could be conflicting deals between other companies. If a company signs a deal with Game A because they believe it aligns with their goals and brand image, they're not going to then want to see their logos within a game they don't believe they match, even if to the creator of the livery it's free advertising. It's not advertising everyone wants.
The vast majority of people are obviously not planning to use copyrighted marks in this way, or even do it intentionally, but companies don't have infinite time and resources to find them all, which is why they usually operate under an automated system (see Youtube) or rely on user reports.
I do agree broadly speaking that copyright laws need serious work for the modern digital era but there is definitely a lot of genuinely good reasons that they need to be exist and able to be protected in some ways.