@mvalle This feature is available in the latest JabRef 5.15
You can set a custom cite command in the preferences for Push To Application and then this will be used when you select the option from the context menu:
From the docs:
With that, you can even support Pandoc’s Markdown citation syntax. Configure it with
[@key1,@key2].
Pushing to external editor application | JabRef
Best regards
Christoph