tandem steering geometry has the same issues as a single. If you get too much flop, then the bike likes to turn. I'm dealing with that right now on one of my bikes, an All City Macho Man Disc. It has 71.5 hta and 45mm rake which means 20mm flop. When I stand up, it really doesn't want to go straight. I'm building a fork with a lot more rake to counteract this and to work better with a handlebar bag. So, yes, start with the steering geometry and get that right. Then the top tube lengths, then everything else falls into place

You don't have to line up the top tubes, but you also don't want the bike to fold in half. The front seat tube needs to be beefed up at the junction. And this is why most tandems have diagonal structural elements.