One more update on this subject. pfSense is still stable with zero up/down events since limiting to 5Gbps.
My TrueNAS box, on the other hand, started showing the same behavior (at the same 5 min intervals) after a software update. They were happening about 1x per day, but even though only one interface in the lagg would go down at any given time, I'd measure some packet loss, likely because smokeping is also on a 5 min interval. This was a change from previous observed behavior where the up/down events would occasionally happen, but not on the 5 min interval and no measured packet loss.
I picked up a Dell X710-T2L for a song on ebay (seriously, like $30 shipped) and cross-flashed it to the Intel firmware. I replaced the X540-T2. My intention was to also limit to 5Gbps but I haven't had to do that. The events just stopped and 0% loss since then. It's even more puzzling because the cabling here, while short, has multiple excursions into wall-mounted jacks with Cat6 (not Cat6a) running under the house through the crawl space. That was not the case with pfSense, which is directly cabled to the switch with Cat6a patch cables.
Don't really know what to think about this other than that 10GBase-T is a crapshoot.