Here is what I get
Used Rubi for the indefinite integration part, since it gives simpler anti-derivatives, (no complex numbers show up). Then took the limits (assumed proper integrals)
solR = Int[Int[Int[1/Sqrt[x^2 + y^2 + z^2], x], y], z]
Gives
(-(1/2))*z^2*ArcTan[(x*y)/(z*Sqrt[x^2 + y^2 + z^2])] -
(1/2)*y^2*ArcTan[(x*z)/(y*Sqrt[x^2 + y^2 + z^2])] -
(1/2)*x^2*ArcTan[(y*z)/(x*Sqrt[x^2 + y^2 + z^2])] +
y*z*ArcTanh[x/Sqrt[x^2 + y^2 + z^2]] +
x*z*ArcTanh[y/Sqrt[x^2 + y^2 + z^2]] +
x*y*ArcTanh[z/Sqrt[x^2 + y^2 + z^2]]
Now just took the limits, one at a time
solR2 = Assuming[Element[{z,y},Reals]&&x2>x1,
Simplify[Limit[solR,x->x2]-Limit[solR,x->x1]]]
solR3 = Assuming[Element[{z,x1,x2},Reals]&&y2>y1&&x2>x1,
Simplify[Limit[solR2,y->y2]-Limit[solR2,y->y1]]]
solR4 = Assuming[Element[{x1,x2,y1,y2},Reals]&&y2>y1&&x2>x1&&z2>z1,
Simplify[Limit[solR3,z->z2]-Limit[solR3,z->z1]]]
And the result is
(1/2)*(z1^2*ArcTan[(x1*y1)/(z1*Sqrt[x1^2 + y1^2 + z1^2])] + y1^2*ArcTan[(x1*z1)/(y1*Sqrt[x1^2 + y1^2 + z1^2])] + x1^2*ArcTan[(y1*z1)/(x1*Sqrt[x1^2 + y1^2 + z1^2])] -
z1^2*ArcTan[(x2*y1)/(z1*Sqrt[x2^2 + y1^2 + z1^2])] - y1^2*ArcTan[(x2*z1)/(y1*Sqrt[x2^2 + y1^2 + z1^2])] - x2^2*ArcTan[(y1*z1)/(x2*Sqrt[x2^2 + y1^2 + z1^2])] -
z1^2*ArcTan[(x1*y2)/(z1*Sqrt[x1^2 + y2^2 + z1^2])] - y2^2*ArcTan[(x1*z1)/(y2*Sqrt[x1^2 + y2^2 + z1^2])] - x1^2*ArcTan[(y2*z1)/(x1*Sqrt[x1^2 + y2^2 + z1^2])] +
z1^2*ArcTan[(x2*y2)/(z1*Sqrt[x2^2 + y2^2 + z1^2])] + y2^2*ArcTan[(x2*z1)/(y2*Sqrt[x2^2 + y2^2 + z1^2])] + x2^2*ArcTan[(y2*z1)/(x2*Sqrt[x2^2 + y2^2 + z1^2])] -
z2^2*ArcTan[(x1*y1)/(z2*Sqrt[x1^2 + y1^2 + z2^2])] - y1^2*ArcTan[(x1*z2)/(y1*Sqrt[x1^2 + y1^2 + z2^2])] - x1^2*ArcTan[(y1*z2)/(x1*Sqrt[x1^2 + y1^2 + z2^2])] +
z2^2*ArcTan[(x2*y1)/(z2*Sqrt[x2^2 + y1^2 + z2^2])] + y1^2*ArcTan[(x2*z2)/(y1*Sqrt[x2^2 + y1^2 + z2^2])] + x2^2*ArcTan[(y1*z2)/(x2*Sqrt[x2^2 + y1^2 + z2^2])] +
z2^2*ArcTan[(x1*y2)/(z2*Sqrt[x1^2 + y2^2 + z2^2])] + y2^2*ArcTan[(x1*z2)/(y2*Sqrt[x1^2 + y2^2 + z2^2])] + x1^2*ArcTan[(y2*z2)/(x1*Sqrt[x1^2 + y2^2 + z2^2])] -
z2^2*ArcTan[(x2*y2)/(z2*Sqrt[x2^2 + y2^2 + z2^2])] - y2^2*ArcTan[(x2*z2)/(y2*Sqrt[x2^2 + y2^2 + z2^2])] - x2^2*ArcTan[(y2*z2)/(x2*Sqrt[x2^2 + y2^2 + z2^2])] -
2*y1*z1*ArcTanh[x1/Sqrt[x1^2 + y1^2 + z1^2]] - 2*x1*z1*ArcTanh[y1/Sqrt[x1^2 + y1^2 + z1^2]] - 2*x1*y1*ArcTanh[z1/Sqrt[x1^2 + y1^2 + z1^2]] + 2*y1*z1*ArcTanh[x2/Sqrt[x2^2 + y1^2 + z1^2]] +
2*x2*z1*ArcTanh[y1/Sqrt[x2^2 + y1^2 + z1^2]] + 2*x2*y1*ArcTanh[z1/Sqrt[x2^2 + y1^2 + z1^2]] + 2*y2*z1*ArcTanh[x1/Sqrt[x1^2 + y2^2 + z1^2]] + 2*x1*z1*ArcTanh[y2/Sqrt[x1^2 + y2^2 + z1^2]] +
2*x1*y2*ArcTanh[z1/Sqrt[x1^2 + y2^2 + z1^2]] - 2*y2*z1*ArcTanh[x2/Sqrt[x2^2 + y2^2 + z1^2]] - 2*x2*z1*ArcTanh[y2/Sqrt[x2^2 + y2^2 + z1^2]] - 2*x2*y2*ArcTanh[z1/Sqrt[x2^2 + y2^2 + z1^2]] +
2*y1*z2*ArcTanh[x1/Sqrt[x1^2 + y1^2 + z2^2]] + 2*x1*z2*ArcTanh[y1/Sqrt[x1^2 + y1^2 + z2^2]] + 2*x1*y1*ArcTanh[z2/Sqrt[x1^2 + y1^2 + z2^2]] - 2*y1*z2*ArcTanh[x2/Sqrt[x2^2 + y1^2 + z2^2]] -
2*x2*z2*ArcTanh[y1/Sqrt[x2^2 + y1^2 + z2^2]] - 2*x2*y1*ArcTanh[z2/Sqrt[x2^2 + y1^2 + z2^2]] - 2*y2*z2*ArcTanh[x1/Sqrt[x1^2 + y2^2 + z2^2]] - 2*x1*z2*ArcTanh[y2/Sqrt[x1^2 + y2^2 + z2^2]] -
2*x1*y2*ArcTanh[z2/Sqrt[x1^2 + y2^2 + z2^2]] + 2*y2*z2*ArcTanh[x2/Sqrt[x2^2 + y2^2 + z2^2]] + 2*x2*z2*ArcTanh[y2/Sqrt[x2^2 + y2^2 + z2^2]] + 2*x2*y2*ArcTanh[z2/Sqrt[x2^2 + y2^2 + z2^2]])
screen shot

Quick verification
solR4/.{x1->2,x2->3,y1->1,y2->5,z1->3,z2->9}//N

NIntegrate[1/Sqrt[x^2+y^2+z^2],{x,2,3},{y,1,5},{z,3,9}]

Assumptions->{x2>x1>0,y2>y1>0,z2>z1>0 }
? (sorry cant test) It should at least fail faster.. $\endgroup$