Good news, it seems. I started digging around to see if it is possible to compensate for z-axis deflection/bend through in my intended software which is linuxcnc and it seems this is theoretically possible:

"The probekins kins module is a trivkins module with optional Z correction. By default, probekins behaves like the trivkins module.

The purpose of probekins is to aid milling slightly warped workpiece surfaces, or deal with a machine imprecision, like for instance when milling a PCB when the board is not ideally horizontal after clamping, or slightly bent or warped. The idea is to probe the actual surface at several points covering the whole milling area, and generate Z correction values from the probed values by interpolating between neighbouring points."

From: http://wiki.linuxcnc.org/cgi-bin/wiki.pl?ProbeKins

Seems good enough for a start although this particular one seems to be using a linear interpolation. Anyway that means that I will not worry too much about the z-axis bend through for now as long as that is not large enough to cause other issues like, for example, stuck leadscrews or excessive wobble.