I disagree with that the toolkit should do rescaling. It makes completely sense to only accept normalized values since it follows the UNIX principle. It makes also a simpler contract to assume that the viewport size always stays within [-1 1]. Some extra work on the client maybe, but much cleaner. You do not expect an audio daemon (jackd) to scale sample values for you, do you? If you give jackd values outside [-1 1] it will clip the signal.

This is a known problem but it has a solution:

From the manual
    Caution: The FLTK toolkit uses single precision variables internally which limits the maximum value that can be displayed to approximately 10^{38}. If your data contains larger values you must use the gnuplot toolkit which supports values up to 10^{308}.

The solution is to not pass values directly to FLTK. First scale them to fit within [-1,1] and draw the axis with labels formatted from the original values. The choice of feeding directly have other bad effects which occurs for time series with a fairly large offset (see figure). It is strange that line drawing is affected but not points.