This is a known issue, and it only affects command line sequencing using the powershell cmdlet. It does not affect loading the template in by hand using GUI sequencing.
The issue was addressed in the ADK 1703 sequencer, which only helps if you want to sequence on Windows 10 1703 or above. I do not expect to see a bug fix for the 5.1 sequencer (only security fixes, and then only if you are really lucky).
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 )