Most probably because the background colour forms an important part of the brand identity for that app.
There are a few apps around that can let you create transparent tiles for some of those apps - look for one called "Start Perfect", and there's plenty of others.
I know there's plenty of apps out there, but WHY MS nor Nokia doesn't want to make it especially for their own apps like Skype, Nokia Camera, Blink, One Drive, Office????? WHY???? It's also their own OS.
I'm sure they keep it like that to make their apps easier to find
and to be honest, I'm not a fan of using Start Screen background, so if you guys want every single app in this world to have transparent tile, I would be the ******* that opposes