It seems like trying to detect device height to ensure that your elements sit halfway under a floating element would be getting into a whole can of worms, so I'll offer a couple solutions that would remove the need for that:
Stick the CTA to the left or right of the screen
If it's positioned without the standard content margin, then it won't appear to be a part of the typical scroll region. This could help to indicate that it's not a part of the screen beneath it.
Obviously, ensure the content will scroll high enough so that all of the content can move comfortably higher than the floating CTA.
download bmml source – Wireframes created with Balsamiq Mockups
Show the CTA after a short delay
Alternatively, you could load the page, then fade or slide in your CTA so that users see that the page extends beneath it (hard to show in a mockup, but hopefully you get the idea).