For sure you can. The problem I ran into was that if I set the pressure for the cuts in Onyx, which is the only way I found to do two unique cuts if one isn't specifically FlexCut, by the time I got to the cutter I'd inevitably want to add more or less pressure but couldn't, because they're locked in when you RIP it. Versus if you use just the default ContourCut and FlexCut (and tell it not to override the plotter) you can adjust both of those on the fly while cutting.
(A good example is if you have more than one cutter, or need to change the blade between when you RIP and when you cut, your pressures are not likely to be ideal on both machines or because a sheep blade uses less pressure than a dull one.)
I only recently gave FlexCut another shot specifically for cutting the outside rectangle of sticker sheets (or whatever) and was mostly pleasantly surprised. I get your trepidation though.
If you find a way to use something other than FlexCut, AND can adjust both at the cutter after it's been ripped, definitely come back and let us know.