For confidential clients, there are scopes assigned to clients and the logged in user has to consent to them. Since there is client secret involved in exchange of auth code for access token, no one can impersonate them and take advantage of their scopes.
But when it comes to pkce flow on a native app, if I had someone else's clientId (clientIds are not considered private information) which has a lot of scopes, I could just start the flow with with their clientId. What is stopping a hacker from using some reputed clientId in the PKCE flow and have access to all their scopes?
NATIVE CALLBACK METHODS
If you look at RFC8252, certain types of callback URL can be registered by more than one app, meaning only a client ID needs to be stolen in order to impersonate a real app, as you say.
This still requires a malicious app to trick the user to sign in before tokens can be retrieved. And of course each app should use only the scopes it needs, and prefer readonly ones. After that it depends on the type of native app.
MOBILE
A mobile app can use Claimed HTTPS Schemes via an https callback URL to overcome this. It is backed by App Links on Android or Universal Links on iOS. Even if a malicious app uses the client ID, it cannot receive the login response with the authorization code, because it will be received on a URL like this, and the mobile OS will only pass this to the app that has proved ownership of the domain via the deep linking rehistration process:
DESKTOP
For desktop apps there are gaps, since only Loopback and Private URI Scheme callback URLs can be used. It relies on users to avoid installing malicious apps. Eg only install apps from stores that require code signing, which also inform the user who the publisher is. If users install malicious apps then perhaps they have deeper problems.
ATTESTATION
A newer technique is to use a form of client authentication before authentication begins. For confidential clients, Pushed Authorization Requests are used, which uses the app's client credential, so this cannot be used by native clients by default.
Mobile apps could potentially provide proof of ownership of their Google / Apple signing keys during authentication, and there is a proposed standard around that.