You can have two [Files]
section entries. One for all *.rar files and one for all files except *.rar, where one of them will have nocompression
flag and the second one won't:
; entry for all *.rar files
Source: "*.rar"; DestDir: "{app}"; Flags: nocompression recursesubdirs createallsubdirs ignoreversion
; entry for all files but *.rar
Source: "*"; Excludes: "*.rar"; DestDir: "{app}"; Flags: recursesubdirs createallsubdirs ignoreversion