Hello Teun,
Because you told me that you not interested in any commercial software I did not answer. But if anyone whants to know if there is software to read IFC to native Creo Elements objects you can see a result of this below.
A model loaded in BimSight.
The same model converted to Creo
Off course it is possible to export Assemblies to IFC object. If you are familiar with BIM you must ask youreself what is the level of detail (LOD) i want to use. In the most common software where you can export a model to IFC there is no possiblity to chance the LOD for the several parts in the assembly.
In the industry in which i work the IFC (from the contracter) has to import to CoCreate/Creo and save it to a inseparable. Before we have the IFC-import module we import all 2D AutoCad drawings and pull it up. We can only attach our models to the building if the reference is there. Do you understand how many hours it takes to reach this....Import a IFC was the first goal to achieve (for our Company).
In the IFC that I convert there was only one assembly structure. The description in IFCSite and IFCBuildingstory where "undefined", it was flat!
When the model is ready we must export the assemblies (and parts) to IFC. You can export the model to STEP and then convert it for example in HiCad to IFC. But that's not the way you want to do it, the IFC model grows to al very large one!
Not only the complex parts should be swapped but also the construction details (how we make the several parts and how we connect them in our assemblies) must not been written in IFC. I totally agree what you have described.
Maybe you can show me a model (or send) so that I can see if it is possible to export your model to IFC with the software I have programmed.
Best regards.
Here a example from a IFC where the following structure is created in Creo, the parts which are created with a outercurve pattern and are the same are also shared!!
I'm down with IFC (Yeah, you know me!). 
(Sorry, a little "rap" humor from the early '90's)
