The following info comes from a third-party Switch developer who wishes to remain anonymous...
I remember the Digital Foundry experts to have been puzzled how some of the worst framerate issues seem to occur so randmoly, not area-specific. I believe these are not the fault of the game, but of the Switch trying to periodically auto-connect to WiFi where there is no network available. This is supposed to happen in the background, but it apparently does affect the game(s).
I actually noticed this in FAST RMX first, where I got periodical FPS drops, while everyone was always saying that it is a perfectly locked 60 FPS experience. It wasn't game breaking, but it made me curious. Driving in circles also made the periodical nature so much more apparent.
Then I also had these in Setsuna, which to me made no sense at all, especially after watching DF's comparison to the PS4 version, where they also said the Switch version was perfectly locked 30 FPS.
Having them on multiple games like that, and in none of them they made sense, got me thinking. At home I turn on WiFi only when I need it basically, so it's not always available. During the Setsuna session I checked the status LED and sure enough it was off. I then delved into the Internet settings of the Switch, found the "Auto Connect" option and turned it off, and Voilà, no more FPS issues in Setsuna and FAST RMX! And only the "usual" minor ones in BotW in very specific (foliage intensive) areas, no more heavy random ones.
While this is just a rumor for now, here's some equally interesting info. If you utilize Flight Mode on your Switch, or turn off your wifi, the issues with framerate go away. While this is just a temporary workaround, word is Nintendo already knows of the issue and is working on a fix. Thanks to Dakhil for the heads up!