When I make lone star quilts, I will machine sew everything up until nearly the end. The last steps, adding the inset squares and triangles, then putting quarters together in to halves, then the half into the whole, I hand sew. For the inset squares and triangles, sometimes I hand baste them in and then finish the seam by machine sewing.
I haven't made much else with Y-seams, but hand basting the tricky areas and then machine sewing is how I think I would handle them in general, especially if there are a lot of bias edges to work with.