So, it that motherjones.com article you link, it's clearly BPA they are talking about, an additive to plastic, not plastic itself.
I don't know if that means that "BPA-free" is often deceptive advertising, or it's referring to different additive that's technically not BPA but problematic for other reasons, or what. (Bear in mind, as a layman, my mindset on this stuff is that the burden of proof should be on proving safety, not on proving harm.)