Even not always these discharges are necessarily waste, but, accidental leaks that occur despite the existing controls in the handling of this type of substances, which can cause adverse environmental impacts on the surrounding environment.

but后省略了they are, accidental leaks是but后分句的表语。逗号提示这里有省略。that引导定语从句修饰leaks，所以that并不多余。

如果删去that, 虽然后面也可以成为一个句子，但无法解释but后的逗号。

其实本句not always由于强调而前置了。恢复正常词序则为：

Even these discharges are not always necessarily waste, but (they are) accidental leaks that...

即 Sth is not A, but B结构，只不过B带了一个定语从句而已。