It looks like a discretization problem. It can be circumvented with CountourPlot3D:
Manipulate[Show[{ContourPlot3D[{x^2 + y^2 + z^2 == 16 \[Pi]^2,
(x - 2 \[Pi])^2 + y^2 + z^2 == 4 \[Pi]^2},
{x, 2 \[Pi], 4 \[Pi]}, {y, -2 Sqrt[3] \[Pi], 2 Sqrt[3] \[Pi]}, {z,
0, t1}, ContourStyle -> Directive[Red, Opacity[0.3],
Specularity[White, 40]], Mesh -> None],
RegionPlot3D[x^2 + y^2 + z^2 <= 16 \[Pi]^2 &&
(x - 2 \[Pi])^2 + y^2 + z^2 >= 4 \[Pi]^2 && x == 2 \[Pi] &&
t1 >= z >= 0,
{x, 2 \[Pi], 4 \[Pi]}, {y, -2 Sqrt[3] \[Pi], 2 Sqrt[3] \[Pi]}, {z,
0, t1},
Mesh -> None,
PlotStyle -> Directive[Red, Opacity[0.3], Specularity[White, 40]]],
RegionPlot3D[x^2 + y^2 + z^2 <= 16 \[Pi]^2 &&
(x - 2 \[Pi])^2 + y^2 + z^2 >= 4 \[Pi]^2 && z == 0,
{x, 2 \[Pi], 4 \[Pi]}, {y, -2 Sqrt[3] \[Pi], 2 Sqrt[3] \[Pi]}, {z,
0, t1},
Mesh -> None, PlotPoints -> 60,
PlotStyle -> Directive[Red, Opacity[0.3],
Specularity[White, 40]]]},
AxesLabel -> (Style[#, 15, Blue] & /@ {"X", "Y", "Z"}),
Axes -> True, Boxed -> False, BoxRatios -> Automatic,
ViewPoint -> {-1, -2.4, 1.}], {{t1, 0.00002, "Value (t1)"},
0.00001, 2 Sqrt[3] \[Pi], 0.00001},
ControlPlacement -> Top]