“Do your initial things in RawTherapee, like demosaicing, perhaps denoising, perhaps other stuff, then send the file as 16-bit to an image processor…”
For graduated filter: Picture Window Pro 8, a replacement for Photoshop and now donation-free from Digital Light & Color, has a Gradient function for this. The column of image transformations is flexible, so you can do a Gradient, do another one right away or after a contrast change, etc.