In your example, you mentionned FTP, but it could be any value, as long as the user can change it.
And yes, then the y-axis could be expressed as a percentage.
User input of wattage (could be FTP, max power, etc) : 350W
Display on y -axis (Absolute[W] or Relative of user input [%]): Relative
On the graph, let say I'm at 210W, I would see 60% (since 210W/350W = 60%).