that pipe is being there since day one about , 50 years ago , all the previous roofers knew how to solve the problem , I'd looked like an idiot if I moved the pipe , the pipe is not the problem the problem is the roofer that don't know to do that detail, that pipe will never leak even if it's the center of the valley.
nothing wrong with the pipe , as a roofer you should know what to do in that case, all the previous roofers did a good job and never leaked, the roof was old that's why the roof was replaced.
I would have and have made my own pipe boot outta galvanized sheet metal, and make my valley outta the same material, then solder all the seams, but hey whatever works is the right method, as long as it doesn't leak after you're done with the install, that's all that matters. When people get in the comments of videos like this saying shit is wrong, hey if i install something, and i put my name behind it, and i say it's done and it's never going to leak, then it's done and it's never going to leak. I've been a roofer for close to 34 years, mostly do metal work these days, box gutters, bay windows and such, like the metal work i did that I'm using for my profile pic here, again tho, it's not wrong if it works brother.!!👍👍