How are you modeling the two pipe branches? If I understand your question, you want the cut to follow the non-horizontal pipe section. Is that a correct interpretation? To do this just start a sketch on the end of the non-horizontal pipe, draw a circle that is the dimension of the cut, and extrude the cut Up to Next. Hopefully that's what you're asking...
it is the chamfering which is causing the issue, i.e for weld prep as we have to get this wye tested and approved which includes a welding procedure...
Can you build the part by starting with a solid, shelling the solid, and then splitting the separate bodies off to create your individual pieces? This way you wouldn't have to worry about cutting individual pieces perfectly to allow them to match up.
Start with two "raw pipe" components. Position them in an assembly. For each pipe, create 3D sketches in-context to represent the other pipe's centerline and OD. This will give you the basis for creating the cuts you need.
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