Confusions with dynamic paired collection creation in tools - tool wrapper XML

While trying to produce dynamic paired lists from a tool I encountered some issues and came across an interesting behavior where I'm not sure if it's due to my limited understanding of how the underlying things work, or if it is indeed weird:

I tried to follow and apply [this example file](https://github.com/galaxyproject/galaxy/blob/master/test/functional/tools/collection_creates_dynamic_list_of_pairs.xml) to my wrapper, and for some reason it never wanted to work out. It seems that having a paired collection as an input somehow changes how the tool works - adding a dummy paired collection input to the above mentioned example file changes the output, even though in my expectation nothing really should have changed. You can try it if you add for example the following input:

```

```

So I'm wondering: What is this dummy input changing in this example file that it won't create the `Duplicate list` anymore (or as expected multiple times for each item in the input collection), but instead only the hidden single elements?

@jmchilton Maybe you can shed some light here as the author of #538

Start with test/functional/tools/collection_creates_dynamic_list_of_pairs.xml and reproduce its behavior with the dummy paired collection input described in the issue. Trace how the tool wrapper handles paired collections and compare the resulting collections. Done means the behavior is explained and, if incorrect, covered by an appropriate regression test.

Written by the indexing model from the issue text.