Fixes related to structures

Issue addressed

Fixes #141 and some other small things

Explanation

Again, several bugfixes applied in the Santa Cruz branch, mostly related to duplicate structures and compound structures. This PR contains those fixes, and also some new tests for bridges and culverts.

Checklist

[X] Updated tests or added new tests
[X] Branch is up to date with main
[X] Tests & pre-commit hooks pass
[X] Updated documentation if needed
[ ] Updated changelog.rst if needed <-- only some fixes so no update?

Additional Notes

It currently does not include test cases checking if duplicate and compound structures are handled well which is something to include. For this, I think it can be a test only for the workflow and not the setup_methods which are already covered by the two new tests.

When developing the tests, I ran into some trouble, see https://github.com/Deltares/hydromt_delft3dfm/issues/168 . This is addressed by also calling setup_channels in the test as a workaround, as I think this issue is too large to fit in this PR. I've included links to the issues in the tests as a reminder for us, and will also link the tests in the issue itself

Deltares / hydromt_delft3dfm