Shadowed dependencies with custom Setup.hs

I am afraid I don't have a small reproducer for this and it doesn't happen on my machine, but have a look at this [Travis build log that failed](https://travis-ci.org/quasicomputational/mega/jobs/328764804). #3503 fixed this problem elsewhere, but maybe it was incomplete for custom Setup.hs components?

Start with the linked Travis build log and compare the failure with the fix in issue #3503, focusing on custom Setup.hs components. Determine how the dependency shadowing occurs and whether it can be reproduced. Done means the custom Setup.hs case no longer produces shadowed dependencies, with regression coverage if the repository provides a suitable test location.

Written by the indexing model from the issue text.