You know when you get something stuck in your head and you won't be able to forget about it until you've solved the problem? I'm like that with this....
You do not need to seel the enclosure to tray inside the cubicle, most manufactures instructions will specifically tell you not to. If you sealled both sides and water did get through the inner seal you'd have a water trap all under the enclosure.
The installer should of run a continual bead of Silicon on the upright fixings before pluggin and screwing them to the wall. I find it best to run two continuous beads parallel with one another.
Understanding the tiles are cut a little close to the tray i can still see from the picture sealant between tray and
tile that has spread well enough to cover the 1mm gap you mention. This should be sufficient in anycase.
What is the tray made of? All though you can't see much of the bathroom in the photos the tiles used, and in particular the enclosure looks to be of good quality. I would presume that a stone resin tray was used? This shouldn't flex at all. The tray's right on the floor so if the floor is allowing a stone resin tray to flex i'd start getting concerned about the floor tiling! So i don't think it's your tray moving.
Lastly, and this is the real head scratcher. In the photos you indicate in red that the areas there are dry? Particularly where the tray meets the tiles on the OUTSIDE of the enclosure. If these areas are dry when the water is pooling on your floor then i would be 99.99% certain your looking in the wrong place for your leak. It won't be coming from the enclosure.
Take a friend and a torch into your bathroom. One of you spray water on the into the corner working from bottom to top. The other, with the lights off look for water running outside the enclosure with the torch (trust me you'll find the smallest drip doing it this way).
Once you've found it (if it's the enclosure) strip back a good amount of the sealant and leave to dry out for 24 hours. Then re-seal.
Hope that helps. Good luck