I was thinking more specifically of things like having to configure HiDPI settings differently for Qt and GTK, for example. There are also some copybuffer inconsistencies at times. It's not a big deal for anyone who is motivated to deal with it, but probably irritating enough to make some people give up early on even if they would otherwise like having a system that's configured properly.
Oh yes, I agree, DPI settings should be global accross the system as much as possible and copy buffer should definetly work consistently. Generally it's the application's responsibility to implement the tie in to these platform systems - on the interface level that should preferably not be tied inseparably to any UI code).
To me however, this is on a different architectural level than how the UI itself is inplemented (which, technically, is just motion graphics with hotspots, but psychologically is the most important part for most users).
