Why are 端母 and 知母 considered as distinct initials in Early Middle Chinese even though they share same 上字's such as 都 or 丁, while 幫母 and 非母 are not?
As we know that 知母 did not exist in Old Chinese. It was later derived from 端母 in Middle Chinese.
The milage that a word differentiating 知母 from 端母 varied in Middle Chinese. Some changed to 知母 in Early Middle Chinese but some did not. And 樁 finally went to 知母.
Due to the vastness of the ancient empires, we must beware that Early Middle Chinese was not a single language but a collection of close related languages at that time. For example, the spoken language in 金陵 was somehow different from that of 長安. The capitals of empires changed during the long period of Early Middle Chinese. 知母 might appear in one place but not in another place.
陳澧 tried to reconstruct 切韻 from 廣韻. He only followed that 樁 is 都江切 in 廣韻. Here 都 is 端母 and so 樁 is 端母 in 切韻. It is up to the correctness of 廣韻.
But after 廣韻, another rime book 集韻 changed it 株江切 and it is 知母.
By the time of 廣韻, 三十六字母, the 36 initials, including 非母. But some centuries earlier, a copy written in 敦煌 was only 三十字母, the 30 initials, indicating that 非母 did not exist at the time. Thus the distinction between 幫母 and 非母 did not exist in Early Middle Chinese.
While 切韻 was vanished long ago, there is a revised version of 切韻 namely 刊謬補缺切韻 which has a few surviving copies nowadays. This helps to verify the correctness on the works of 陳澧.