You can place windows vertically or horizontally. I prefer horizontal and that's fine.
Yes of course I can. Thankfully, they at least allowed us to move windows.
But I'd prefer same-window trace display. Maybe there are use cases when having math in a separate window is better (FFT is an example), but if you use, for example, two channels and A-B math as a poor man's differential probe, then the resulting trace must definitely be drawn in the main window along with the direct input, as you may naturally want to correlate that math waveform with something on the third channel, for example. Having it in a separate window as the only option defeats half the purpose of having the math function.
I'm not even mentioning that the windows borders and titlebars, when they are placed horizontally, consume the precious vertical space, which is already in great shortage with huge sections of the screen dedicated to the upper and lower status/control bars. This makes the useful vertical space of the two windows (main and math) ridiculously small, bordering uselessness.
As for the eye movements, it's very funny ... I don't have any problems.
There's nothing funny. Forcing the user to shift focus, unless it is a natural part of the flow in question, is bad, it's that simple. Good UI designers know this and place related elements in such a way that they are all can be seen and read without a single movement of the eyeball. An example would be the central section of a car's dashboard, a wristwatch, or winamp's main window.