You've intuited correctly: clear and neutral are indeed the same. People buy colored creams for more than one reason:
1. They may wish to alter the color of their shoes somewhat.
2. They may need to cover scuffs and the like, which neutral doesn't do well.
3. Neutral can darken some light leathers, which light-colored creams won't (strange, isn't it?).
So if I had a pair of tan colored shoes and wanted to keep the same color, should I try to find an exact match (or the closest) shoe cream OR should I save myself the trouble and use "clear" or "neutral" shoe polish?