It might be rust, it might be varnish.
Tomos tanks collect really badly at the bottom, and then there is almost a divider on each side of the bottom part of the tank. Shine a bright flashlight in there and you'll see.
I'm gonna guess you have a giant chunk of stuff at the bottom. You want to get a pressure washer and absolutely bomb it at that bottom corner of the tank and try to free up the cluster of old crap. Do it with a friend and flip the bike upside down and dump what you can out the fill hole. Repeat 10x or so.
Then use your chemicals and repeat the process as many times as necessary.
Evaporust is basically a converter, so you really shouldnt get any "rust" coming back after you eradicate whatever mess is at the bottom.