The black strip caulk I had wasn't really enough and it looks like it broke free from the front corners of the rail caps.
I think I'm going to do what that truxedo installer said was necessary with factory rail caps. He said he uses clear silicone around the edges of the rail caps to keep the water out.
The little bit of strip caulking was just enough for the holes on the cover rail corners. It wasn't meant for sealing anything but the cover's rail corner section.
What surprises me is that there aren't more people complaining of leaking.
Here's a picture of where the leaks are. The red circle is where the black strip caulking is suppose to be used for the cover's rail corner section, to seal out water.
The problem is the circle in blue. That's the bulk header that's not covered by the rail caps or the bedliner. The water gets on the bulk header and runs under the bedliner section and under the rail cap. The bedliner has the yellow angle pointed at it's starting edge. So you literally need to apply silicone to all these edges that are included in the black circle. The black circle extends a bit away from the corner but the rail cap here still lifts a bit where water can get under it. Also the back section, by the tailgate, has opening where water can get under the caps. I used foam tape to cover those gaps.
I guess I'm more disappointed in Nissan for not paying attention to this water problem area for those of us that don't want an open bed.
Well the real problems seem to be just at the front and rear corner, so the caps are relatively easy to silicone. I'm thinking now that my other covers, Nissan Tonneau OEM cover, and the Pace-Edwards corner leaks weren't the fault of the covers. However, the Pace-Edwards leaked everywhere, the corners were just one spot. The Nissan OEM Cover had warped rails creating gaps in the center of the rail for water to come in plus the darn thing ripped while trying to close it.
It all makes sense now, why I have had so many water leaks, while other people I know never had these water leakage issues with their different trucks

.
Have a good one.
I guess I should mention, even if you had a cover where the rails are on top of the rail caps, the front section still will allow water to come in under the rail caps, so no cover is immune except maybe a total bed rail covering hard tonneau cover or bed cap (topper).