Hi Chez,
The maximum allowed custom entities depends on our subscription license, so it is organization level, while the application could be just regarded as user interface to show data.
We can go to Advanced Settings > Administration > Resources In Use to check the number of allowed custom entities.

The limit can be extended by contacting Dynamics 365 technical support.
Therefore, a custom entity can be exposed in any application: for example, we can still view segment records in Sales Hub by replacing URL parameter with logical name of segment entity even though the entity is not enabled in Sales Hub by default.

In other word, to expose an entity in a specific app, we just need to open that app in App Designer, then enable the custom entity and add it to Site Map.
Regards,
Clofly