The only possibly valid reason to not use a hypochlorite source of chlorine with an SWG is if you were to shock to a higher level without lowering the pH first. By shocking with hypochlorite, the pH rises and that could cause more scaling in the SWG cell, but if you lower the pH first then you minimize this effect (and if you are using 50 ppm Borates then the pH rises by about half as much). If you are just adding enough to help out the SWG keep up for some unusual demand or until you get to adjusting the on-time, there should be no problem.
Just remember that when adding a concentrated chemical such as chlorine or acid to the pool, you should do so by pouring slowly over a return flow (preferably in the deep end, especially if you have a floor drain) and then lightly brush the wall and floor in the area where you poured to ensure thorough mixing.