Apologies to those having taskbar problems, it is related to the window centering code.
It takes the screen real-estate minus the task bar, to compute the offset for window centering. If your selected windowed resolution is the same as desktop, go ahead and turn that feature off.
The official release of 0.2.0 will fix this.
For now, I would suggest using the dxgi.dll from
here and the tweak tool from
here. Go to the
Graphics tab and make sure
Center Window is unchecked, also turn
Aspect Ratio Correction to
On.
The HUD Stretch feature is not something you are locked into, by the way. The INI setting is just how it will start, you can always press
Ctrl +
Alt +
Shift +
. to toggle it in game, I find this necessary to hid visual artifacts on the sides of the screen (will be fixed in a later version).
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I do not monitor these forums often, so it is easiest for me if you could post anything on the Steam forum post for the project.