Quick update on my experience post-repair regarding the Dynamic Iris flickering/pumping issue on my RS-540.
After over a month of regular use the issue has still not come back, with one predictable exception.
I still can't believe how good the image looks, and how phenomenal the iris operation is. It's essentially invisible to me in normal viewing. In fact, I've had to glance up in the lens on occasion just to verify that the DI is in fact operating at all.
The one exception, which is previously documented, is that after getting a 4K Apple TV, my PJ would sometimes be shutdown in HDR mode and power on in SDR. As my HDR and SDR modes use different manual iris settings, this will cause the manual iris to lose it's position on the track, and the DI will go a little haywire in this instance. Cycling the manual iris all the way down and up will correct the issue (you'll hear it almost grind for a second as it's forced back into alignment). I fixed this by setting my universal remote to always flip the picture mode to natural before power off, so it always powers off and on in SDR. Since doing that I haven't seen any issues with the DI.
To recap, while in repair JVC replaced the manual iris to solve what I was perceiving to be a DI issue. The repair has (at least in the short term) completely resolved the intermittent pumping/flickering I was seeing with the DI. I'll be sure to post if the issue re-occurs in the future.