We have the exact same setup with the rubber tube extending the aluminium part and a lip seal on top. It's not a flexing issue, the rubber tube is really just a short piece of large diameter exhaust hose, extremely tough, but still somewhat flexible. It will easily absorb what little movement there is (and there isn't much to begin with).
I'm not sure how the aluminium tube is attached to the top of the housing. Maybe it's actually threaded onto the remaining thread above the nut? On ours no thread is visible either. Not sure how much JP3 diagrams can be trusted
Either way it looks like you now have crevice corrosion and likely pitting from the leak, which can only be fully treated from the outside (with the rudder out). Depending on how severe it is, you might have to replace the housing or might be able to patch it up with epoxy. Until you can haul out, I'd meanwhile clean and dry it best you can and apply a thick bead of MS polymer sealant between the top of the nut and the tube, going for a large surface area to adhere to. This has lasted us 6 months when we had a small trickle (from the last metal through-hull, not rudder) before we could haul out and fix it properly. Epoxy based filler will not work well with the water leaking in (it's great in the other direction though - outside the boat, but you'd have to drop the rudder for that!).