Quit Pages v6 on macOS Sierra.
In El Capitan, and macOS Sierra (Pages v5.6.2, and V6 respectively), the custom user templates are stored in the following location in a User Templates folder.
home directory/Library/Containers/com.apple.iWork.Pages/Data/Library/Application Support
In the Finder, you must right-click on the com.apple.iWork.Pages package folder, and select Show Package Contents to continue downward into that hierarchy. Once you are in that Application Support folder, then click Launchpad : Other: Restore to launch the Time Machine Restore facility. It will open to the same Application Support folder on your Time Machine backup, as you have selected on your Mac.
Still in Time Machine, look inside the User Templates folder. If there are templates in there, then select the User Templates folder, and click Restore. If the folder is empty, move back in time by each backup until you discover templates, then click Restore.
Launch Pages, New document, and observe your restored User Templates, which Pages Template Chooser refers to as My Templates.