You can also use a hardware token to handle the encryption/decryption (yubikey/nitrokey/GnuPG smartcard/...).

If you have a trojan on your computer it'll still be able to decrypt your passwords while the token is plugged and unlocked of course, but at least offline attacks shouldn't be possible. Of course that doesn't mean you shouldn't use 2FA wherever possible to mitigate the risks further.

Some tokens can also be configured to wait for a physical button press to allow the decryption which which can help prevent a complete background decryption of your passwords (assuming that each password is stored with a different key, like with password-store for instance).

I guess if your system is compromised then password security becomes gravely threatened, no matter how secure the password manager may be. The only partial solution I can think of is to have the OS sandbox every application from every other.

Yep, pretty much. It really reminds me of this: https://xkcd.com/1200/ for obvious reasons.

The only ways I can think that would be able to prevent this are:

     1. Physical non-networked device password manager
     2. Really creative usage of SELinux
     3. QubesOS

And in reality, #1 is kind of how RSA tokens are used. Of course, physical can be lost, stolen, and all that. QubesOS takes a ton of resources to run effectively, given everything is VM'ed and contained with a capability system.

In all honesty, I could see buying an Android at a Pay as You Go place, and repurpose it to be a offline password manager. Never connect it to wifi, BT, cell. And any APK's you need you load via microSD card and USB.

Yes, the way to deal with trusting password managers is to use TFA as much as you can.