To be honest i see this more as a feature than as a problem.
This will very likely improve the quality of the linux build making it more complete and compatible with the windows build and features.
Just compare the linux and windows versions of firefox for example.
They look far from the same.
And for a big part this is caused by the difference in toolkits used beneath the skin.
Now i am a big fan of QT.
But even if they port their own: one toolkit everywhere can only make things better.