For example, given a package A that depends on package B and package C, where package C also depends on package D - is there a way to output this information? (Using a vendoring tool or otherwise)
The vendor.yaml output by govend doesn't include transitive dependency information - neither does the Gopkg.toml file
output by dep, from what I can see. The go.mod file produced by Golang 1.11's mod and does annotate some dependencies as // indirect - but it does not annotate dependencies with any information about which dependency they were pulled in via.
Did you try https://github.com/KyleBanks/depth? It does provide a decent dependency tree at first look I tried.