Many of the advantages that Toolbox gives can be mitigated on the server side, rendering the tool less useful.
Dialog doesn't let you skip all quests. The majority can't be skipped, and those that do are mostly in Cantha. The Gate NPCs mostly check if the player completed the previous mission, not the previous quest.
The slightly larger map range that Toolbox gives could also be mitigated on the server side, by not giving the client information about spawn until they're actually within the normal radar.
Open chests on distance? Yes, I'm sure an additional constraint could be added that the player actually have to be within X distance.
/chest: Either they could add that command into the game, or put a similar constraint that you have to be within X distance to be able to access the Xunlai Chest.
There are more features in ToolBox that I'm not so sure about how they could be affected.
Personally I hope they inspire a but from the good options from ToolBox rather than block them. By adding similar features ingame, there's less incentive to use a thirdparty program.