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If you're interested in a 2d view in the end, just choose some projection direction, apply the projection to your points, and do a point2d; or see if viewer='tachyon' will give something acceptable.

If you want a 3d view, given that point3d gives you spheres, you might as well plot spheres yourself and choose the radius; hopefully you can choose a smaller radius than the one given by point3d; or you could explore what sage.plot.plot3d.shapes2.Point actually does and try to hack some variation.