Unable to use Ember data with JSONAPI and fragments to support nested JSON data

Overview

I'm using Ember data and have a JSONAPI. Everything works fine until I have a more complex object (let's say an invoice for a generic concept) with an array of items called lineEntries. The line entries are not mapped directly to a table so need to be stored as raw JSON object data. The line entry model also contains default and computed values. I wish to store the list data as a JSON object and then when loaded back from the store that I can manipulate it as normal in Ember as an array of my model.

What I've tried

I've looked at and tried several approaches, the best appear to be (open to suggestions here!):

Fragments

Replace problem models with fragments

I've tried making the line entry model a fragment and then referencing the fragment on the invoice model as a fragmentArray. Line entries add to the array as normal but default values don't work (should they?). It creates the object and I can store it in the backend but when I return it, it fails with either a normalisation issue or a serialiser issue. Can anyone state the format the data be returned in? It's confusing as normalising the data seems to require JSONAPI but the fragment requires JSON serialiser. I've tried several combinations but no luck so far. My line entries don't have actual ids as the data is saved and loaded as a block. Is this an issue?

DS.EmbeddedRecordsMixin

Although not supported in JSONAPI. I sounds possible to use JSONAPI and then switch to JSONSerializer or RESTSerializer for the problem models. If this is possible could someone give me a working example and the JSON format that should be returned by the API? I have header authorisation and other such data so would I still be able to set this at the application level for all request not using my JSONAPI?

Ember-data-save-relationships

I found an add on here that provides an add on to do this. It seems more involved than the other approaches but when I've tried this I can send the data up by setting a the data as embedded. Great! But although it saves it doesn't unwrap it correct and I'm back with the same issues.

Custom serialiser

Replace the models serialiser with something that takes the data and sends it as plain JSON data and then deserialises back into something Ember can use. This sounds similar to the above but I do the heavy lifting. The only reason to do this is because all examples for the above solutions are quite light and don't really show how to set this up with an actual JSONAPI set up that would need it.

Where I am and what I need

Basically all approaches lead to saving the JSON fine but the return JSON from the server not being the correct format or the deserialisation failing but it's unclear what it should be or what needs to change without breaking the existing JSONAPI models that work fine.

If anyone know the format for return API data it may resolve this. I've tried JSONAPI with lineEntries returning the same format as it saved. I've tried placing relationship sections like the add on suggested and I've also tried placing relationship only data against the entries and an include section with all the references. Any help on this would be great as I've learned a lot through this but deadlines a looming and I can't see a viable solution that doesn't break as much as it fixes.