The problem is simple. They have to fit inside the heat shield designed for the original exhaust. Or you'd need to try to bend/alter the existing heat shield to fit.
KTM openly state (for example) their Akrapovitch will NOT fit.
And frankly I don't think many KTM 790/890 Duke (esp R) purchasers bother with panniers. Those that do probably need more space. IIRC they are pretty small.
A solo rider will probably go for a seat bag. Or use a seat rack and fit a top case. A two-up rider may find the capacity lacking.
If your plan is to leave the panniers on - Why spend money on a flashy pipe?.
I know it's NOT a Duke - I know - really I know. Something I am coming to terms with is that for DISTANCE with LUGGAGE - a mid-sized ADV is probably what "I" should have.
I have been through the same issue with my luggage choice. I ride with a nice Wings pipe. It's an aesthetic choice. But there's no getting away from the fact that the original pipe has an excellent heat shield. I have looked at all sorts of custom heat management options - But in the end - Like
@EvansB2 - with luggage I'll use the OEM pipe.