this opens up the ability for the amps to drive the drivers differently at low levels among other things.
The information linked is not stating different operation at low levels. It is stating that the analog portions of the active circuit use low signal levels as opposed to "speaker" levels.
w.r.t. Using the Genelec software, don't you have the Lyngdorf incorporated in your Genelec system? GLM Grade will have better tools for analysis of individual speakers allowing you to better tune their position and if you incorporate acoustics, allow you to measure and tune those as well. However, you need to pick whether the GLM software or Lyngdorf is going to do the room correction including timing and level.
Ya, I don't know why I didn't think of crossovers as moving and changing per impedance, frequency, amplitude.
Well they better change with frequency and impedance or they would not work :-). Much of the work in driver design the last decades has been to ensure linearity w.r.t. voltage so this is not as much of an issue as previously, but see my points previously w.r.t. linearity. Moving the crossover to the signal domain whether digital or analog solves the issues of non linearity of the driver interacting with the crossover, but not the inherent linearity issue. Many of Genelec points, point to the greater ease, flexibility, and consistency possible with an active design.
You also have the issue of the driver parameters changing with time as they heat and cool. This is more important for professional speakers as they are more likely to run at high levels for extended periods, but as @lonemountain stated, that market is not resistant to active speakers.