The short answer is because you may not want to divulge that these two files are, in fact, identical to an adversary with access only to the ciphertext. Here are some additional details:
The standard symmetric encryption algorithms, such as AES, encrypt a basic unit of a “block”; in the case of AES, this block is 128 bits, or 16 bytes, long. Used in its simplest form, the Electronic Codebook (ECB) mode, identical blocks of clear-text encrypt to identical blocks of ciphertext; the ciphertext can thus leak information about the structure of the file. Moreover, if additional protection is not implemented, if an adversary knew that, say, the boss’s salary information was in one block, and his own in another, he could swap those two blocks of the cipher-text and be assured a higher salary, without actually knowing the key. Of course, having a separate key for each block would solve that problem, but would create a key management nightmare. These problems have been extensively studied in the cryptography literature. In general, only one key is needed for each group of files under the same access control policy (typically, belonging to the same application, or being in the same directory tree).
Both Server General TDE and Server General KMS have been designed so that identical files when encrypted do not result in identical ciphertext.