OK I see the problem. The underlying problem is that the GL-Transitions are not true transitions in Shotcut. To perform a true transition you need to be able to access the 2 images in the clips that are transitioning. With WebVfx this is not possible. The upper image (e.g. that on V2) is available, but not the lower image (V1), so I had to change the GL-Transitions to only use the upper image.
On some transitions (such as Swirl) this does not matter, while on others, such as Bounce the transition does nothing at all. This is not a deficiency in the GL-Transition filters per se, The problem is that there is no mechanism for WebVfx to pass the second image, so that it can be operated on.
By making judicious use of Shtocut’s own transitions and then applying the GL-Transitions filter to the resulting transition, it is possible to mask some of the problems, but not all unfortunately. Have a look at @sauron’s video to see what can be done. There is even a page-curl on there: GL Transitions made using Elusien's GL transitions overlay generator