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Pomeroy has ten switches, one per app, and all ten start off. Nothing is requested from macOS, and no tool is served, for an app you leave off.

A toggle and a grant are two different things

This distinction matters, because they can disagree.
The toggle is yoursIt records what you want Pomeroy to do. It lives in Pomeroy’s settings, and Pomeroy obeys it. Switching an app off takes its tools away from every assistant immediately.
The grant is macOS’sIt is the operating system’s answer to a permission request. macOS owns it, stores it, and is the only thing that can take it back — in System Settings → Privacy & Security.
So switching Calendar off in Pomeroy does not revoke the Calendar grant. It stops Pomeroy using it. If you want the grant gone too, take it back in System Settings; Pomeroy will ask again the next time you switch that app on. Both gates have to be open for a tool to run. If either is shut, the assistant gets a plain refusal that names the switch to flip.

What each app asks for

Switching an app on is the only thing that ever triggers a macOS prompt, and it prompts only for that app. Maps and Weather have no prompt of their own: MapKit and WeatherKit answer any app that asks. For those two the toggle is the entire gate, which is why they still start off.
Mail, Notes and Shortcuts are asked for separately. macOS prompts once per app Pomeroy sends an Apple event to, so approving Mail says nothing about Notes. You will see up to three prompts, not one.

Messages is different

Your messages live in one file, ~/Library/Messages/chat.db, which macOS guards behind Full Disk Access. Pomeroy does not ask for Full Disk Access, and will not. It is one switch that would hand Pomeroy every file on your Mac — your mail, your browser history, your backups — in order to read one database. Instead, switching Messages on opens a standard file dialog at ~/Library/Messages with chat.db already selected and every other file greyed out. You hand over that one file. Pomeroy keeps a read-only bookmark to it, and holds no grant over anything else on your Mac. The full reasoning.

What Pomeroy will never ask for

Two grants are permanently out: Accessibility and Screen Recording. That refusal is worth more than a promise, because you can check it yourself. Open System Settings → Privacy & Security → Accessibility. Pomeroy is not in the list, because it never asks. It costs real features — knowing which window is frontmost, attaching a screenshot to a support report — and they are declined on purpose. Why the refusal binds the grant, not the use.

Changing your mind

1

Open Settings

Click the Pomeroy icon in your menu bar and choose Settings.
2

Switch apps on or off

The same grid from setup. Switching an app on for the first time asks macOS for its grant; switching one off takes its tools away at once.
3

Take a grant back, if you want to

Go to System Settings → Privacy & Security and remove Pomeroy from the relevant list. Pomeroy reads grants live and never caches them, so it notices straight away.
You do not need to restart your assistant after changing a toggle. The tool list stays the same; what changes is whether a call is allowed through.