I think they should be made like that from the factory. This issue and the so-called standard has been around long enough. This changed should have happened over a decade ago. Same can be said for the USB 3.0 header. RIGHT ANGLE Adapters people it isn't that hard to do. But let's save that dollar because we need it and make the end user suffer.
There might be a few that it will not work for. That is going to be a given. They can include some adapters to go back to bring it straight up for you. I try to choose boards that the layouts are nice. Sounds like you have an ITX board maybe? If that is the case they are the Devils playground. But I like a challenge it is a good thing.