3rd party app that opens zoom meetings does not follow waiting room rules

It sounds like there is a gap in the other app. Zoom provides a robust API but it sounds like the appointment app you are using does not factor waiting room settings when scheduling Zoom meeting (waiting room would need to be set to true when the API call is sent scheduling the meeting). There are therapy appointment apps that let you schedule Zoom meetings that follow your waiting room settings. One option is Salepager, a Zoom app that lets you schedule Zoom therapy meetings that honor your waiting room settings.