Some examples of the difference would be helpful.
showInSymbolList
Optional. Links symbols to the local symbol list. Valid values are 0 or 1. If 0, the corresponding symbols will not be displayed.
<key>showInSymbolList</key>
<integer>1</integer>
showInIndexedSymbolList
Optional. Links symbols to the global symbol list. Valid values are 0 or 1. If 0, the corresponding symbols will not be displayed.
<key>showInIndexedSymbolList</key>
<integer>1</integer>
Reference: http://docs.sublimetext.info/en/latest/reference/symbols.html#settings-subelements