First, the intensity output probably is TTL only. The Intensity output is really made as an adjunct to the normal color lines, for things like PCAOMs. If you have only a single color laser, we would always recommend using a real color line to control it. For years -- since the Amiga days, following on through the LD/QM32 days, we recommended people simply use the "red" output. For LD2000, you can use literally any line since the color system is more train-able. For the FB3, we would recommend using the red output, and then telling the software (in projector settings) that you have only a single color laser.
There is a differential board available. It's the size of a postage stamp. The FB3-XE (external edition) already has this integrated, but the FB3-SE (board-level "secure edition") may or may not have it. Basically, you have to tell us you want it at the time you order, or purchase one later on.
But in any case and every case, it is only the X and Y which are differential. Color signals are not and so this would not affect your Intensity output in any case.