A remark on my configuration shown above: Using Adobe RGB for the color space as input to the stitcher results in unnatural flat colors. Seems that the stitcher is not correctly doing color management. So use sRGB instead. This restriction should also be documented in the manual. Or even better, it should be fixed! Working in a Lightroom/Photoshop environment without supporting color management is a no-go!
BTW: The THETA desktop app also handles colors poorly so don’t depend on it for color proofing. For quick previews after exporting the equirectangular image from Lightroom, I use mostly use FSPViewer which handles ICC profiles correctly.