Well, there is nothing really "magic" about the content of the team invitation notice; it is easily created.  My team uses a custom application to request/approve/create/remove Jazz Project accesses.  The process on the create step sends an email whose partial (redacted) content is:

========================================================================
For the RTC Eclipse Client ONLY

In the RTC Client choose File & Accept Team Invitation. Copy the invitation below and paste into the Accept Invitation text field. Do not include the "Start" and "End" lines.Start of Invitation

teamRepository=https://rtp-rtc7:9443/jazz
userId=theuser@dom.com
userName=John
projectAreaName=Requested Project Area
End of Invitation

Should be easy to do in your work flow if your automation adds the ID to Jazz.