I can't find any occurrence of the string '$(Auto)' in any of the path statements/lists I'm afraid.
If anyone has a similar issue here is what I did to get to a solution,
Set the project options (as well as the IDE options) search path to
C:\Users\Public\Documents\Embarcadero\Studio\21.0\Bpl
for each off IcsCommonNewRun and IcsVclNewRun and IcsCommonNewDesign and IcsVclNewDesign in turn.
They all now compile/build and the Designtime ones install
BUT
The BPL name in each case contains the string '$(Auto)' rather then the substituted package version number.
e.g the built bpl filename is IcsCommonNewDesign$(Auto).bpl
Renamed each bpl to the desired name e.g. IcsCommonNewDesign270.bpl
I then used the package list [Component | Install Package] to add them to the IDE.