When sequencing, and while in monitoring mode, move the shortcut to the Start Menu\Programs\IT. It doesn't matter if you use per-user or per-machine while in monitoring mode.
Then App-V will lay down the shortcut to the expected start menu based on publishing type (user or machine, but for your use you'd want user based publishing).
Your external solution to redirecting the start menu should be respected by the App-V client.
I will note that if you are using App-V 4.6, Notepad++ has a trick to sequencing in that the package name cannot include the "+" character. This isn't an issue in App-V 5 but, just in case, want to make sure you are looking at
the right issue.
tim
Tim Mangan MVP for App-V and Citrix CTP Author of AppV books: "PowerShell with App-V 5 (5.1 Edition)", "The Client Book (4.x)" and "OSD Reference Book" (http://www.tmurgent.com/Books )