The installation of executables to `lib/<pkgname>` instead of `bin` for the `ros2 run` command doesn't affect the location of libraries. Therefore I don't think this is related.
In general you don't have to modify any environment variables if you do call the setup file (which will do that for you).
Maybe you can post more information, what the exact error message is as well as the steps you are doing. E.g. a reproducible example might help to give you more specific feedback what might be causing the problem.
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