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So I found out that the issue here is not with the order the images are stitched but rather the rotation that is estimated for the camera parameters in the Homography Based Estimator and the Bundle Ray Adjuster.
Those rotation angles are estimated considering a self rotating camera and my use case envolves an user rotating the camera (which means that will be some translation too. Because of that (i guess) horizontal angles (around Y axis) are highly overestimated which means that the algorithm considers the set of images cover >= 360 degrees which results in some overlapped areas that shouldnt be overlapped.
Still havent found a solution for that problem though.
