Surprisingly for 'si checkpoint' there is no documented flag for "Apply Label to all Members"
like the corresponding dialog from the gui.
If I would not have that flag in the gui I would try
1.) Checkpoint the project eg. with label 2016_12_06_BUILD1
2.) Determine the the Project revision that was created (the one with label 2016_12_06_BUILD1)
3.a.) Retarget the sandbox to that project revision (this only works if your checkpoint source was from a root sandbox)
or
3.b.) View/Open the created build project from the project history view
4.a.) Apply Member->Properties->Add Label to the retargeted build sandbox.
or
4.b.) Apply Member->Properties->Add Label to the opened Build Project
The b. Variant is more generic but I guess it's harder to translate into cli commands.
(you will likely have to deal with exact repository location resp. configuration paths on the server side)
From a sandbox perspective my approach for 1.) (without concern for change package issues) would be:
c:\prj1_sandbox>si checkpoint --label=2016_12_07_B111 --description=JENKINS_BUILD_111
This will create labels only on subprojects.
For a retargeted build sandbox my approach for 4.a.) would be:
c:\prj1_sandbox>si addlabel --label=2016_12_07_B111 --recurse
This will add labels to the revisons of the corresponding build project too.
Regards
Juergen
BTW: If you find a solution how to translate this all into cli commands in the context of the jenkins configuration, I would be interested too 