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The stitching module does assume internally that an input image is a photo. This fact is used when camera parameters (such as focal length, aspect ratio, etc) are estimated. But if you give a panorama image instead the camera parameters estimation step won't fail immediately. It can even return something close to actual parameters, but there's no any guarantee on that.

If you want to stitch images one by one, as you described, then you can build your own image mosaicing pipeline. The stitcher class is a pipeline built on top of a lot auxiliary classes, all of them are avilable in the cv::detail namespace.

Regarding the mosaicing confidence threshold. As I said too low values may lead to incorrect behaviour. If changing this parameter doesn't help, you can try to decrease Stitcher::panoConfidenceThresh.