field collection v seperate content types
Good question, but hard to answer. I can't tell you what to choose but I hope my thoughts will help.

If I understand your needs correctly, Field Collection definitely has some advantages. Firstly, field collections are purpose built to be related to other entities. Each field collection entity is always related to one (and only one) node. That seems so match your use case, although I wouldn't know how if it's easy to add multiple field collections to multiple nodes at once. In my experience, field collection provides a pretty smooth way for site maintainers to add new data, so that's good.

The downside of field collections is that many contrib modules are still node-centered. For every site you build, it's hard to predict which problems you will be solving or which features you will be adding 6 months after the launch. If you decide to use field collections, you may find yourself in a situation where you want to add something that would have been really easy with nodes.

Since you're exploring different solutions, maybe you should also look at Drupal Commerce, if only for inspiration. It's a really flexible system which adds line item entities to orders more or less like you want to add charges to properties.