First is the app lock-in, which perhaps hasn’t bitten you but not everyone is so fortunate, especially in a scenario the article describes, corporate environments where you can’t install arbitrary software onto the machine you use.
The other problem is corruption. I haven’t experienced this in a few years, but it’s certainly not unheard-of for a binary data file to experience corruption; often the only way to recover it is to perform surgery on it, which not everyone will have the tools and skills to do.
Plain text files are much safer in that regard.