Signal is finally tightening its desktop client's security by changing how it stores plain text encryption keys for the data store after downplaying the issue since 2018.
It’s true that full-disk encryption is useless against remote execution attacks, because the attacker is already inside that boundary. (i.e., As you say, the OS will helpfully decrypt the file for the attacker.)
However, it’s still useful to have finer-grained encryption of specific files. (Preferably in addition to full-disk encryption, which remains useful against other attack vectors.) i.e., Prompt the user for a password when the program starts, decrypt the data, and hold it in RAM that’s only accessible to that running process. This is more secure because the attacker must compromise additional barriers. Physical access is harder than remote execution with root, which is harder than remote execution in general.
No, defense in depth is still important.
It’s true that full-disk encryption is useless against remote execution attacks, because the attacker is already inside that boundary. (i.e., As you say, the OS will helpfully decrypt the file for the attacker.)
However, it’s still useful to have finer-grained encryption of specific files. (Preferably in addition to full-disk encryption, which remains useful against other attack vectors.) i.e., Prompt the user for a password when the program starts, decrypt the data, and hold it in RAM that’s only accessible to that running process. This is more secure because the attacker must compromise additional barriers. Physical access is harder than remote execution with root, which is harder than remote execution in general.