Interesting. There seems to be a slight performance hit. I assume it could be from the flatpak sandbox.
7.5018 [dev_process_image] pixel pipeline took 3.285 secs (7.412 CPU) processing `_DSC9187.NEF''
But this is not really the problem you are seeing. In your .deb setup (4.4.2), I think you have the resources set to very fast GPU. The preview pipe is being processed in GPU and it takes 0.9s. The flatpak is setup to default. In default, it uses the CPU for the preview pipe and it is taking 4.5s.
Therefore, change the flatpak processing preferences to very fast GPU.