yeah, jason, I went thru this with a customer a few weeks back. Toyota used 2 pumps on the 3vze. One with and one without a bypass tube. This seems to be the only difference, so cap it and run it if you don't need it.
How would you recommend capping that bypass tube? definitely not something I'd want coming off/out. Also, do you know where the bypass tube goes? I'm just curious as to why the tube is even there