Also, the keys don't have to reside on the same device the password store is on. If you have one key per client device for example.
So to protect against that, don't use a password manager. Which means that you're more likely to re-use passphrases, because lots of them are hard to remember and keep straight. So breaking one gets access to many others.
My head spins.
Sure, in general, you want to avoid password reuse to isolate password compromises / security breaches (some companies are still storing passwords in plaintext in 2016, ugh). But in this case, we're talking about private keys that should never leave your local machine. If those are compromised (even passphrase-protected), then it's not inconceivable to think that your password store might also be compromised.
Yeah, reliazed that, my post was just my "logical" progression.
If you are going to use a password manager to store them there's no point in using different passphrases.