We seem to keep showing up on the same threads Brian. As you know, I'm the Dream in Blue skin author, and that was part of the reason I was asking the OP which skin he was using.
Unless you want to go nuts with massive upscaling (which will screw up how things look overall as you noted) to increase the size, the height is dependent on how much space each skin author has allocated for the player bar. There is finite space available for the two lines of track info and the track progress bar/waveform below it. If you increase the text size as you have done, it decreases how much space is left over for the waveform. The screenshot below shows my setup with smaller fonts for the track info, and as you can see, the waveform is a fair amount taller. The OP could decrease the track info font size even further (in the XML file) to increase the waveform height even more, but then the text would be pretty small.