It's certainly true that TNN can sometimes just 'get you', though I think that that can be said for even some of our most positive match ups tbh.
Chalice is definitely more of an issue for the Duke BUG deck and I've found that our deck really overwhelms their abrupt decays, making Chalice even better. Yes, they run daze but they are easily the worst daze deck in the format - I've noticed the play pattern of: They daze my thing, I wasteland them next turn, they reach three mana way too late, occurring pretty regularly. I can concede JTMS is a beating, though the games they reach four mana that easily are surely the games they've managed to just get away from you anyway.
I've found a more proactive approach of powering out something problematic quickly, as opposed to trying to answer everything they have, to be a more successful mentality against them. Loam is fantastic at navigating narrower board stalls, and powering out big Knights or a Scooze can be really annoying for them when you're threatening to kill them on the crack back.