4 Tormod’s Crypt
4 Ground Seal
3 Troll Acetic
2 Naturalize
1 Ground Seal
1 Silklash Spider (tech)
A small point that is easily corrected, but you have 5 Ground Seals listed in this sideboard...I'm assuming it should be the Root Maze you alluded to later in your post.
I think Drop of Honey is interesting but not sure if it's what this deck needs. It already runs Ground Seal for Goblin Welders and has Naturalize for TNT's fat, and as you mentioned it is on the slow side. Against other aggro decks it might be difficult to break the inherent synergy in the card.
Zealots are a natural inclusion in the deck, but I am not convinced Emerald Charm is better than Naturalize unless you have been having problems with a Chalice OT Void set at X = 2. The additional flexibility the Charm gives you buy untapping creatures and making other creatures lose flying is far less useful than the artifact removal you get with Naturalize.
For the most part I think a list like this is adequate, but now that the deck is being played more (you only have to look at the TMD Open results) I think it may be worth dedicating some SB space to cards that will just win the mirror matchup that would also be useful against other aggro decks, which Stompy is less prepared to deal with than it is against control.
One card that looked interesting to me was Dawnstrider: you could feed it endlessly with Squee, it's tutorable via Survival, and Stompy on the other side of the board will have a lot of difficulty dealing with it. It could also be potentially useful against other aggro/aggro-control decks that are light on removal, like GAT, Madness, and others, to buy you a lot of time.
In addition, in the mirror match, Stompy in its present form lacks a strong finisher that would be able to punch through a stalemate, instead relying on Survival to just overwhelm the opponent. However, when both players are relying on the same strategy, it becomes a less desirable strategy that, left alone, leaves luck as the determining factor. I am not sure if the manabase could support it but Silvos came to mind for addressing this issue. If you're able to run Silklash Spider in the SB, I'd think it could support 1 Silvos too.
These are just some preliminary thoughts. I might consider siding 1 Dawnstrider, 1 Silvos, and one other "bullet" creature in the space that you're trying to make room for Drop of Honey because they would both help against the mirror match and be generally useful against most other aggro and aggro/control decks as well.