microG being disabled but present is still enough for some apps to work, which makes sense given that you can disable Google Play Services on the stock OS.
Google's Play client libraries are still used on CalyxOS by the apps using Play services. The Ads SDK is a fat library and works without Play services. Only the Lite variant of that has a hard dependency on Play. GrapheneOS isn't giving any additional access to Play when it's installed compared to what the client libraries have available.
WhatsApp is clearly a proprietary service too, and CalyxOS is integrating that into the Dialer app. Signal's server source code is not fully public either and went a whole year without even the incomplete releases that are now available again. Both are centralized, third party services integrated in a special way not available to other apps. Isn't that the problem with Play services? It is from our perspective.
They'd also be used on GrapheneOS, and anywhere else basically.
> WhatsApp is clearly a proprietary service too, and CalyxOS is integrating that into the Dialer app.
The integration is entirely done into the open source Dialer app and generic enough that it could be extended to any apps that have phone numbers. Signal and WhatsApp are simply the most popular amongst those.
The issue is that you're giving Google services privilege and integration not available to other apps.
Disclaimer: I've only read the linked webpage.