you BoM a TR playing Durations, then Bonfire the Durations. the BoM still stay in play until the Durations finish all effects, right?
Bonfire messes up tracking and has not been fixed (the fix would be adding "non-duration," which still doesn't fix all cases, e.g. you can Bonfire the Throne that played a Duration) (edit: no the fix is what dbclick said, the Improve trick of seeing if the card would be discarded) (or I mean, just limit it to Coppers). If you play a Duration and Bonfire it, you still get the effect. If you Throne a Duration and Bonfire the Duration, the Throne goes away, remember that rule is that it stays out as long as the Duration, and the Duration is gone. But the effect still happens. The effect also still happens if you Bonfire both of them or just the Throne. If you BoM a Throne playing Durations, and Bonfire the Durations, the Throne wouldn't stay out, so BoM doesn't either. Anyway as noted, the Bonfire scenarios where tracking is messed up do not actually happen. We can construct a scenario where you're Bonfiring Hirelings to Graverobber them or whatever, but it's just not a thing.
The rule "Throne stays out with the Duration" has corner cases where everything isn't tracked perfectly. The main one though is storage cards, like Haven / Archive / Gear, where the stored cards themselves handle the tracking, so irl it's not confusing (if you Throne Gear but only set aside cards once, you know just what to do even though a Throne is pointlessly sitting there). If you Throne a Secret Cave and only discard once, or a Tactician and only discard once (e.g. no Pathfinding trick), then Throne stays out but isn't tracking anything.
We discussed fixing all the corner cases. Stef was in favor. The problem is that the rule that covers everything is way way harder to learn/understand than "Throne stays out with the Duration." We've been doing great with the current rule for a few years now. So in the end I didn't change it.