That is the problem with inexpensive timers. That is what the overflow pipe is for so the garden can water the minimum amount of time on your timer. Even though your plant roots only need to be watered then drain.
If you are using
grow rocks then their is no problem watering 30 minutes on 30 off because the rocks hold so much oxygen. And yes you can water less ( 30 on 60 off 30 on ) when the plants, are small. If your plants show signs of wilting at the end of the 60 min. off cycle then you will know to set the timer to 30 on, 30 off.