Hi Georg,
Without having looked at ABE's source code for a long time (which makes any assertion risky), I agree with you. This process was first designed and implemented by Carlos Milovic back in 2005, as a command-line utility using an early version of the PCL. We implemented it as a PixInsight module in 2006, and if I can remember well, the last revision was made in 2007. That means that this tool isn't up-to-date with respect to most processing tools.
I'll try to update ABE as soon as possible, and I see no a priori problem to implement masking for the correction phase of the process. If correctly applied, ABE is a very efficient tool for gradient removal in relatively simple cases; it definitely deserves a complete revision.