Hello.
There are several ways to organize your VFX, the easiest is to add your most used to favourites and just open the favourites tab.
There is also the search option, so you could rename the transitions.
Alternatively you can place them in folders, this will group them, however they will display as the folder name being a prefix. The list will be as long but in sections rather than alphabetical.
You can also remove any you do not use to shorten the list, these can be moved to the Fusion folder in a new folder named as you wish, making them available in fusion only.
You can also create a macro containing multiple VFX (not plugins) so there is 1 entry in the effects library for a category and the selection is in the inspector.
A further thought is you can have them in a floating pop out window as Motion Essentials does, currently this only works well in the fusion page so difficult to implement on a transition pack.
I believe the issue your having is the VFX developer has decided to group them as they did (everyone seems to do this) however the developer could have grouped them as you wish.
Let me know if you require any further help.