It sounds like you have around the same number of artifacts as I do. Maybe it does have to do with my selection of Chalice? I don't know. I may also just be overstating the regularity of Thoughtcast at 2 or less. Perhaps you see it in isolation? What I mean is both Thirst for Knowledge and Trinket Mage are also 3 mana plays, so often times when Thoughtcast would cast me 3 mana I don't really note it because I have other plays that I can make instead.
With Lodestone costing zero mana, you actually have one more card to tutor for it with Tolaria West, which has the bonus of being uncounterable. So this version would have more ways to get the combo over a Spellbomb version.
And I'm not really sure what you mean by using up all your Trinket Mages. Wouldn't it be the same if I ran Aether Spellbomb instead of Lodestone? In normal bomberman builds there is only one card, Spellbomb, that allows a combo win.
I'm not trying to lambast Time Walk. It's restricted for a reason. I could always run Time Walk if I felt it was good for the deck, but now that I run Lodestone Time Walk becomes optional rather than mandatory. And I haven't found it to be better than other options.
I want to throw out another thought on this--you mentioned Negate and Mana Leak at various points. Perhaps this is blasphemy in these parts, but is Mana Drain really superior to either of these counters in Bomberman? I rarely develop a significant advantage off drain mana, and the UU cost makes it too slow against storm. More and more it's better to get Negate online first turn than to sit on a Mana Drain.
To be honest, I have had the same feelings on the subject. Both in terms of wanting to run Negate and feeling that it might be blasphemy to pick Negate over Mana Drain.

But yes, Mana Drain is almost always a full turn slower than Negate. I don't know if I want to be the one to champion it though, especially since my deck is somewhat deviant already. But I wouldn't argue against a decisions to use Negates over Drains.
As far as Canonist goes, that seems rather idealistic. Combo can go with creatures in the sideboard, Tarmogoyf or Negator. Both of which are stronger clocks than Canonist. Meaning you'll still have to counter their spells on top of protecting your own Canonist. I've also seen EE as the sideboard card of choice as well which plays Canonist against you.
But really what are we arguing about on the card? I don't feel it's a suitable replacement for Chalice as Chalice is better in more match-ups, is far less symmetric, is tutorable by Trinket Mage, and does not require a Tundra. As far as the sideboard goes, I could definitely see it being an anti-combo card. But I don't see how it can be a good card for the maindeck, especially considering the bane of my deck is Null Rod. I'm not saying Canonist is a bad card. It's certainly fine against storm and I have considered it for the sideboard, but it does not feel like a main deck card.
I do not sideboard Chalice out very frequently. My sideboard is very much in flux, but I have a good idea of the direction I want to take it for most match-ups. In match-ups where I do not want to play Chalice @ 1, I usually just leave it in and play for Chalice @ 2 (which still only hits 5 cards in the main deck). Aggro, Combo, and Ichorid I usually play Chalice @ 1 for assorted 1 drops, Aether Vial, Duress, Dark Ritual, Cabal Therapy, and other things. Against Oath and Fish I usually play Chalice @ 2 and trade my Mana Drains and Thoughtcasts for Spell Snares and Swords/Threads. I'm not sure against Shops and Slaver/Tezzeret. While Chalice isn't especially good in those match-ups, I'm not sure what I would trade it for as I'm not sure what direction I want to take my sideboard.
Changes to the main deck... Cut 1 Top for 1 Meekstone. Cut 1 Mana Drain for Merchant Scroll. Cut 1 Echoing Truth for Echoing Truth.