There are a few places where shimmed libraries are mentioned in LIBDEPS but without the shim name:

https://github.com/mongodb/mongo/blob/master/src/mongo/SConscript#L138
https://github.com/mongodb/mongo/blob/master/src/mongo/SConscript#L276
https://github.com/mongodb/mongo/blob/master/src/mongo/SConscript#L374
https://github.com/mongodb/mongo/blob/master/src/mongo/SConscript#L839
https://github.com/mongodb/mongo/blob/master/src/mongo/db/fts/SConscript#L40

There may be more.

I think these may prevent making --use-system-all or --use-system-x work correctly, unless I misunderstand something about LIBDEPS and the shim system.