The highlighted joint will indeed place the plate outside the beam flanges, and it doesn't offer an option to offset it along Y axis.
You can either create a manual plate positioned at the specific position, or if you need the "plate" to be along the whole beam length, you can customize a generic compound beam to create an I beam plus two Flat sections. I've attached a sample model with such a section.
More information about how generic compound beams can be configured can be found in the following FAQ : http://www.graitec.com/en/FAQ_view.asp?FAQID=825&Language=EN&Name=How+are+custom+shape+compound+profiles+created+in+Advance+Steel%3F
Attachment: genericcompundbeam.zip