Yes, Markdown has disadvantages, and a few rough edges for uses as the format for editors et al, but there are two very big advantages and/or sideffects of it's widespread use: (1) it's cleartext and therefore very good as a measure against vendor lock-in and (2) it has, to some extent, dampened the rampant "not-invented-here"-esqe tendency to use proprietary formats. Even in open-source apps, proprietary formats make it hard for non-dev users to get their stuff out. If it's markdown (or at least supports markdown export) from the beginning, at least you know you can take your data with you.