@Srinivasa,
You’re correct regarding the astrological aspect as our Sages may have not known about new gemstones that are available today in the market. However, as a very cheap alternative these less priced gemstones (citrine, yellow topaz, amethyst, iolite etc.) can be used instead of costlier ones. Some alternative (based on astrological aspect) is better than wearing nothing at all.
However, regarding chemical composition of gemstones; different family of gemstones have very different chemical composition and properties, crystal structure, inclusions etc. All Sapphire (Yellow, Blue, White, Green, Pink etc.) and Ruby have same chemical composition with little difference in trace elements for coloring agents (which you’re talking about here) as they belong to the same family/parent i.e. corrundum (http://www.gemstonebuzz.com/corundum). However, other gemstones like Emerald which belongs to Beryl (http://www.gemstonebuzz.com/beryl) family is differnet as regard to chemical composition and same goes for other precious and semi-precious gemstones like pearl, coral, diamond etc. which are very different in chemical composition.
But, I agree that for best astrological effects it is best to wear those gemstones which have been mentioned by our Sages in there scared books of astrology. 🙂