Conversions don't just loose metadata, you loose the ability to specify things. LaTeX shines because it can do everything by itself, markdown clearly can't and even with a TeX template you loose much of TeX's power.
You should start out by defining your desired output and needed input. I realize that 99% of document content can be fully realized in markdown, but the 1% can easily be a total deal breaker and make using markdown a complete nonstarter.
You should start out by defining your desired output and needed input. I realize that 99% of document content can be fully realized in markdown, but the 1% can easily be a total deal breaker and make using markdown a complete nonstarter.