You can update the factory image (and your router) to the current Turris OS version using this guide. If you’re still/back on Turris OS 3.x then you might want to go straight for the USB update method described further down in that post.
I can’t speak for the Turris team but I doubt that they will invest much time on the Turris OS 3 → 6 upgrade path. I agree that it might be worthwhile to eventually update the factory image across the fleet.