Very cool tool! A little feedback:

[Nakilon]

With Gemfile like this:

source "https://rubygems.org"

gem "minitest", github: "Nakilon/minitest", branch: "patch"
gem "minitest-around"
gem "webmock"

gemspec

plugin "bundler-graph"

It produces

1. The [[default]] (and [[development]]) might look better at the top level. I don't remember how exactly to make it in dot, maybe via defining subgraphs. I have spent some time tweaking the dot earlier around a similar tool for Homebrew.
2. Maybe there is a way to somehow tell the difference and make it visible which gems are defined in Gemfile and which in the .gemspec
3. On my image there are two arrows to minitest that looks excessive but the reason is that I specify the version of it. Maybe have an option to add the version/ref attached to the edge if defined.

[duckinator]

wrt 3, I think the two lines leading to minitest makes sense: two things are depending on it, and the graph is indicating that you would have to change two things to remove the dependency.

Aside from that, I agree with what you said. 👍