Apps may be better for circumstances where an app may need to store sensitive info securely. For example, the hardware-backed keystore manages the decryption keys for encrypted app data. A PWA cannot interface to it and cannot store data there. I wouldn't trust putting any private keys in a web browser because of the reliance of servers.

Individual apps can also control permissions better than PWA's, as the permissions for the PWAs are given in browser while an app is OS-wide and independent.