I am someone who struggles with sit bone pain in most skis. It is possible in my experience to "toughen up" the bottom over a period of months. But this needs to be done carefully and in a measured fashion. If you force yourself through too much pain you will not have adequate healing by the next paddle, and you will enter an escalating cycle of ever increasing tissue damage and inflammation.
I did this to myself last year. I had to take a month of from paddling due to an injury, then went to the Columbia river gorge for 6 days of 2 downwind paddles a day. I was in my own ski, the most comfortable ski I have ever owned, padded to my exact specifications. Nevertheless, by the end of the week I was in pain every moment I was in the ski. But the runs were awesome and so I toughed it out and kept paddling.
When I got home from that vacation I could not tolerate 5 minutes in a ski or kayak, and could barely sit in a chair at work. I had given myself raging ischial bursitis on both sides. I was in agony and had to take 3 weeks completely off from paddling to let healing occur and inflammation subside.
Once I was at the point in recovery where I could tolerate 5, but not 10 minutes in a ski, I started inventing workouts around that limitation. In one workout I would paddle 5 minutes hard then hop in the water and do vigorous water jogging for a couple minutes next to the ski, remount, and repeat for an hour or so. I also did my own Australian iron man style workouts where I would paddle 5 minutes, swim 5, then run 5 in waist deep water.
I suggest you try to end your workout within 10-15 minutes of the onset of discomfort. If you are still getting worse with that strategy then you need to start getting off the water even sooner, and maybe even take some time completely off.
I agree with your observations about leg length. Straighter legs is usually easier on the sit bones. The downside is that straighter legs require greater posterior chain flexibility to maintain good posture. In addition, straighter legs (especially flexibility is poor) decreases pressure on the footboard, and powerful paddling can only happen when you can easy get firm constant foot pressure.
Current Skis: Nelo Vanquish AIR, Epic V10g4, NK 670 double, NK exrcize, Carbonology Feather, Think Jet, Knysna Sonic X
Former Skis: Epic v10g3, Kai Waa Vega, Epic V12 g2, Epic V12 g1, Epic v10 double, Nelo 550 g2, Fenn Elite S, Custom Kayaks Synergy