[member="Valiens Nantaris"] Hate you and double posts <3 but I'll answer both.
1) I would put it in either or honestly. The market place seems proper because of what it's meant for, but if you're looking for discussions etc, I'd throw it up in the Discussion, just to weigh your options of builders. I know most factions throw their stuff within a pre factory or just ask people they know have the materials/capabilities to make the item you're wanting to build.
2) Thank you for bringing that to my attention, I'll be looking into that. As for now, the answer is no you cannot do that. Apologies for the confusion.
Edit: Technically you can, the flagship template lists examples of what would be considered a flagship. As long as your "unique" ship doesn't fall into the basis of lets say a SSD then you're fine according to the templates. Any more questions on it, its best to discuss and have an open gate of communication with the FJ that is looking over your submission. Keep that in mind, all the templates do have examples of what is considered what.