I found a work around!
Unfortunately I am unable to use the generated Simulink blocks directly (with the drag and drop simplicity) or to load the symbolic expressions to calculate the inertia, coriolis, etc. However, by loading the symbolic expressions into the workspace and opening the variable (which is a struct) I can copy the generated symbolic expressions directly. Thus, making a custom Matlab Function block and computing my copied symbolic expressions I can compute the unknown matrices.
So to calculate the coriolis matrix I have a custom Matlab Function block as follows (the symbolic expressions will differ for your robot):
function C = compute_C_matrix(q1, q2, q3, qd1, qd2, qd3)
%cor1 = load('coriolis_row_1')
%cor2 = load('coriolis_row_2')
%cor3 = load('coriolis_row_3')
c11 = (7569*qd3*cos(q3)*sin(q3))/320000 - (87*qd3*sin(q3))/1600 - (7569*qd2*sin(2*q2)*cos(q3)^2)/320000 - (569*qd2*sin(2*q2))/3200 - (87*qd2*sin(2*q2)*cos(q3))/800 - (87*qd3*cos(2*q2)*sin(q3))/1600 - (7569*qd3*cos(2*q2)*cos(q3)*sin(q3))/320000;
c12 = (87*qd2*cos(q2)*sin(q3))/800 - (167569*qd3*sin(q2))/320000 - (7569*qd1*cos(2*q3)*sin(2*q2))/640000 - (121369*qd1*sin(2*q2))/640000 - (87*qd1*sin(2*q2)*cos(q3))/800 + (7569*qd2*sin(2*q3)*cos(q2))/320000 + (7569*qd3*cos(2*q3)*sin(q2))/320000;
c13 = (7569*qd2*cos(q3)^2*sin(q2))/160000 - (87*qd3*cos(q2)*sin(q3))/800 - (87*qd1*cos(q2)^2*sin(q3))/800 - (87569*qd2*sin(q2))/160000 + (7569*qd1*cos(q3)*sin(q2)^2*sin(q3))/160000;
c21 = (sin(q2)*(80000*qd3 + 7569*qd3*cos(q3)^2 + 56900*qd1*cos(q2) + 17400*qd3*cos(q3) + 34800*qd1*cos(q2)*cos(q3) + 7569*qd1*cos(q2)*cos(q3)^2))/160000;
c22 = -(87*qd3*sin(q3)*(87*cos(q3) + 200))/160000;
c23 = (qd1*sin(q2))/2 - (87*qd2*sin(q3))/800 + (87*qd1*cos(q3)*sin(q2))/800 - (7569*qd2*cos(q3)*sin(q3))/160000 + (7569*qd1*cos(q3)^2*sin(q2))/160000;
c31 = (87*qd1*cos(q2)^2*sin(q3))/800 - (7569*qd1*cos(q3)*sin(q3))/160000 - (87*qd2*cos(q3)*sin(q2))/800 - (qd2*sin(q2))/2 - (7569*qd2*cos(q3)^2*sin(q2))/160000 + (7569*qd1*cos(q2)^2*cos(q3)*sin(q3))/160000;
c32 = (87*qd2*sin(q3))/800 - (qd1*sin(q2))/2 - (87*qd1*cos(q3)*sin(q2))/800 + (7569*qd2*cos(q3)*sin(q3))/160000 - (7569*qd1*cos(q3)^2*sin(q2))/160000;
c33 = 0;
C = [c11 c12 c13;
c21 c22 c23;
c31 c32 c33];
I obtain the symbolic expressions by loading them from their respective .mat files as done in the following code (run in the Command Window), these files are generated by the code generation procedure outlined in the question above:
cor1 = load('coriolis_row_1')
cor2 = load('coriolis_row_2')
cor3 = load('coriolis_row_3')
Then I double click on cor1, cor2 and cor3 (structures corresponding to rows of the coriolis matrix) to find expressions for each term in the coriolis matrix.
Hope this helps =)