Currently, it's not possible to have distinct email templates for different applications within a tenant.

One solution is to use liquid syntax to customize templates per application. While the same template will be used across all applications, you can customize per application this way with application.clientID or application.name.

Here's an example:

{% if application.clientID == "<App1 client ID>" %}
  <h1>Hello from App1!</h1>
{% elsif application.clientID == "<App2 client ID>" %}
  <h1>Hello from App2!</h1>
{% else %}
  <h1>Hello!</h1>
{% endif %}