A signed PDF file is just like all signed files with embedded signatures: the signature itself is excluded from the hash calculation.
Open a signed PDF document in a hex editor and search for string /ByteRange. You’ll find something like this:
36 0 obj <</ByteRange[0 227012 248956 23362 ] /Contents<308226e106092a864886f7
This indicates which byte sequences are used for the hash calculation (position and length of each sequence). So in this example, byte sequence 227013-248955 is excluded, because it contains the signature in hex format padded with 0×00 bytes. This padding is not part of the DER signature, you can change it without changing or invalidating the signature.