Is there any way I can change that?

Lets say I download a style, do some custom changes to fit my need.
Once done, I would like to set it as default style and 'reset' all red and orange marked changes.
So to have a 'clean' style?

Not really. The purpose of the red and orange marks are to let you know which templates are not vBulletin default, so you can revert templates if problems arise from customizations. You can't know you've customized something, if the template doesn't let you know somehow.

You can edit the MASTER STYLE in debug mode to create new default templates. But, honestly, there's no good reason you should ever do that. If you edit a MASTER STYLE template, the changes are permanent. You've now set the default state of your template, and reverting one will just delete it. There's no going back without going through the upgrade process again. That feature only exists for devs to create new templates for their modifications.

I only mention it because it's possible. But it's decidedly not something you should do. Those templates are marked for a reason.

That's sort of what I am ;)

But thank you all very much for your help!