Maybe the option SphericalRegion->True could be of help
Manipulate[
Graphics3D[
{
Sphere[{-Cos[\[Theta] \[Degree]] sep, 0, -Sin[\[Theta] \[Degree]] sep}],
Sphere[{0, 0, 0}],
Sphere[{Cos[\[Theta] \[Degree]] sep, 0, Sin[\[Theta] \[Degree]] sep}]
},
Axes -> False, PlotRange -> {{-2, 2}, {-1, 1}, {-1, 1}},
Boxed -> True, SphericalRegion -> True
],
{{\[Theta], 0, "Angle around Y"}, -180, 180, Appearance -> "Labeled"},
{{sep, 1, "Separation"}, 0, 3, Appearance -> "Labeled"}
]
