The only real "flaw" is that the dark forest theory hinges on the inability to communicate at superluminal speeds, and yet the novel has superluminal communication (siphons). But if you ignore all that, it is a brilliant piece of SF.
If FTL communication is possible, it could be possible to establish the other civilisations intent before they could send anything destructive.
As for the Sophon's it might be that they require a compatible recipient to work and so first require matter to be sent to the distant location. It's a long time since I read the Three Body books, but I seem to remember them being based on quantum-entangled particles, which would fit with this.
Near the end I think future civilizations communicate via dimensional membranes or some magic-technology like that, but it doesn't reveals your position either.