That works quite well, I made a tool that did it similarly a while ago. It basically goes like this... Boolean, select borders, convert to renderable spline.... Youll probably want to normalise the splines if you have high res geometry or they get quite messy. My script copied the uvs generated for the splines into vertex…
Are you baking all this down? You could do this in blender by baking the bevel shader on pre unwrapped penetrating cylinder clones and then apply and bake the welds using decal machine. You don't even need a highpoly. You can project the open ends of the cylinder intersections onto the perpendicular cylinders and use those…