I spent a lot of time in January looking for the same thing and ended up settling on Mermaid.
It’s text-based and takes a little bit of time to learn the syntax, but it’s pretty much everything I wanted in a flowchart tool: free, works on all OSes, and doesn’t require manually positioning arrows or nodes.
The documentation can be overwhelming at first, but you can make a solid flow chart with just the basics.
Example
flowchart LR
foyer{Foyer} .->|#Search foyer for ghosts| ghost_clue(Discover clue about ghosts<br>if Perception > 10)
ghost_clue .-> foyer
foyer <--> living_room{Living Room}
living_room <--> kitchen{Kitchen}
living_room <--> bedroom{Bedroom}
Alternatively, you could try draw.io, yEd, or some of the suggestions in this thread.
In the past I’ve used TiddlyMap, but I’ve been trying to move away from TiddlyWiki. Unfortunately, IMO no other piece of software is nearly as good at organizing story notes, nor has a fraction of its power. And I have tried just about everything (self-hosted MediaWiki, Wiki On a Stick, Notion, Obsidian, Scrivener…)
Fun(?) fact: Twine Sugarcube is derived from an old version of TiddlyWiki and inherited a lot of TiddlyWiki’s syntax.