Can a circuit with three-ways be split in two branches?
Some inspectors will give you a hard time over that usability issue. Three-ways are required in certain hallways and stairways, and an inspector who doesn't know when a three-way is required and when it isn't, might simply reject anything that confuses him.
You can purchase a single yoke device with two three-ways, that physically occupies one gang location in a switch box.. Perhaps you could wire your circuits like this:
             three-way (1a) ===== three-way (2) ===== ceiling-mounted fixture A
panel =====&lt;&lt;
             three-way (1b) ===== three-way (3) ===== ceiling-mounted fixture B