macOS Photos App can definitely mess up Theta files on import and may not always show all files on camera, i recommend never to use this app for anything other than casual iphone snapshots
macOS Image Capture App can sometime not show all image files inside the camera, but i have never seen it mess up the files it does transfer
RICOH THETA File Transfer for Mac is the most reliable method to transfer files from theta camera to mac in my experience
if you want to prevent macOS Photos App from hijacking your camera, open the app w camera connected and uncheck “Open Photos for this device”
also note that Theta stand alone stitcher request for original DNG can be pointed to any DNG from the same camera, it is looking for the per camera custom calibration metadata inside the DNG, so an image from another camera may be accepted but it may not stitch as well as with metadata from dng from that exact same camera