Characters are unified amongst dialects, but pronunciation is different. Different characters could sound different or similar or same under different dialects. There are also specific characters that are only used by certain dialects.

The zhuyin / pinyin system is the phonetic symbols / alphabet plus rules to sound out every character in Mandarin. Then there are many many dialects in China, some with more tones and some with less tones etc etc.

The Chinese language is all so complicated... 

gnilma

ideasfromtheedge

Learn Chinese with Sensei #2: 自由人

cryotosensei

Ok, so the part I was missing is that even though Mandarin characters are not necessarily phonetic, there are phonetic rules that tell the reader how an unfamiliar character should sound.