I've done several frames with those same tubes and slightly ovalizing works well. I've also just rounded the ears with a file and then flattened them slightly to make good contact with the seat tube for brazing/welding. As was already mentioned, you can line up the seat stay joint with the ears of the top tube and flow the fillets into each other to cover the ears of the top tube. Otherwise, it looks just fine with an external fillet that transitions into an internal fillet at the ears, as long as you round the ears nicely before you braze it.
This issue is much easier to deal with if you are welding. This picture is a 35mm top tube welded to a 32mm seat tube.
I'll second the suggestion to push the front end out and run a shorter stem. I'm 5'7" and I design my personal gravel bikes to use a 50mm stem for several reasons, the least of which is toe overlap.