What is the logic behind converting documents to a PDF and then submitting that PDF too. How would that work in practice (potentially there could then be three versions of a document: DOCX, the EPO rendered PDF document & my PDF back-up copy)?

You can, if you wish, file a PDF back-up copy of any application documents filed in DOCX format. The only condition is that you file them in PDF and DOCX format in a single submission. Documents filed in DOCX format constitute the originally filed documents. This is of particular importance when filing an application. The application documents filed in DOCX format constitute the content of the application as filed within the meaning of Article 123(2) EPC. A PDF back-up copy can serve as evidence of what you intended to file (e.g. in the case of a request for correction under Rule 139 EPC).