Interesting, I see that RCOU.C3 dropped at first during the first period of low RCIN.C3 then recovered about half way through, that seems to suggest that it may not necessarily as a exclusive result of the low RCIN.
However I would definitely try with throttle nudge disabled and see if you can still detect the problem.
When I fly in Auto I put my throttle on the Tx at 50% and leave it there but I have no throttle nudge and when I get a failsafe there is no change in aircraft behaviour. I have flown 400hr professionally and regularily flew BVLOS out to 30km, I always turned the Tx off just after launch though, and never saw that. However my THR failsafe was always enabled and set to "continue in auto" else RTL. I wonder if, as that is disabled you're getting some weird effect. But first to test with throttle nudge off to see if it's that.