AFAIK you can only pass cq:page to the publications section given the right template.
What I'm trying to do is drag & drop .article files which are associated with InDesign into
the publications section.
Please advise how I configure this using crdxe or via templates.
Currently there is no OOTB support for .article/.folio files in the way you describe.
Where did you get those files? You could contribute those articles to the same folio outside of AEM if you'd like (articles in a folio coming from both AEM and InDesign).
Final article ordering in the mixed Folio case would be easiest to manage via a sidecar file or FolioProduer UI.