Member Database – use WordPress or keep it separate?

I have a site for a private group of around 300 members. We want to have a robust membership database and I know enough to make my own mySQL database (single table) and output the data with php, so one choice is to keep our member database completely separate from WordPress.

But I read tutorials like this one and about several different plugins that claim to add additional fields to make it possible for us to just add more info on top of the WordPress users we’ll be creating anyway. I am just skeptical about altering a database that WordPress needs to function?

If I use a plugin that allows me to add additional fields to the existing WordPress users database, could that possibly be detrimental to the site? I mean, even if I have to access that data using my own custom coding, I just want to know how safe it is to even be adding additional fields to the default WP user database in the first place?