To say that the total long-term deflection is three times the deflection due to dead load and the deflection due to live load is an approximation only, but I have found it to be a reasonable approximation.
When calculating the deflections in rc structures your approach should follow:
1. Calculate the immediate deflections based on Ieffective, Dead Load and Short-term service live load.
2. Calcalate the long-term deflections based on increasing curvatures due to creep and dead load and long-term service live load.
3. Calculate the incremental deflection as being the difference between the short-term service and long-term load cases.
I think the factor of three comes from the use of a kcs multiplier (creep and shrinkage multiplier). Again, the use of creep-shrinkage multiplier is an approximation magnifier based on testing of heavily reinforced highway girders and should not be used for lightly reinforced (relativley speaking) flat slabs.
The co-efficients comes from the following application where short and long-term deformations are calculated on the following factors:
1. Short-term displacements...
delta_short=G+0.7*Q
2. Long-term displacments...
delta_long=(1+kcs)*G+(1+kcs)*0.4*Q
If the creep-shrinkage multiplier is taken as 2 which it is when no compression steel helps to minimise the effects of shrinkage, then the long-term deformations will approximatley come out to 3*G+1*Q.
Check out 9.5.2.5 in ACI318-08 for the use of long-term deformation multipliers but again, this is only an approximate assumption. I only use it to verify the answers of the rc design package I use.