Ultegra shifting issue
I looked at some pictures of the bike.


The thing that fits most of your symptoms is that when the FD cable is under tension, it does something to the alignment of the guide plate that the cables are wrapping around, pulling it closer in against the frame such that the RD cable suddenly has tension relieved from it and therefore can't make it up to the big cog, and downshifts with more hesitation.
That you say the problem also exists when the FD cable is disconnected completely is curious, because it's a little like saying the problem happens when there's tension on the cable and also when there's not. Maybe that also misaligns or destabilizes the guide somehow.
Barring other options, I would pull the cranks and BB and see what you're working with in there. It's possible something has happend that has caused the guide to not be supported properly. You may be able to feel it happening by putting a finger against the plate while the other hand shifts the front.
Another thing to look at would be if you adjust the RD to be at the right tension with the FD in the big ring, does it have the opposite problem in the other direction? It seems like it probably would, but it's worth checking.
The other possibility I can imagine is that it has to do with the internal crossing. Usually one would assume this symptom wouldn't be caused that way, because one cable becoming straighter under tension could contort another cable crossing it in a way that increases tension to that other cable, but decreasing the tension is hard to see. But, perhaps they're crossing each other near the contact point with the guide plate in a way where it makes that possible. If you can reverse which cable is crossing over the top, it's possible that could fix it or you could at least learn more. Also, most frames like this can have the housings set up to not cross the head tube, and thus have no internal crossing, but it will come at the cost of much less clean housing lines up front and likely more housing rub on the frame.