It doesn't say that low chemistry applies to your team, to simplify it, it essentially says that the difficulty is higher against teams with high chemistry. It's not applying the low chemistry to your team, other game modes against AI do not apply chemistry. As an example, it's basically saying that legendary mode on career mode does not have chemistry involved, so facing a team with high chemistry in squad battles may feel more challenging.
It's not about them applying the opposing teams chemistry to you, with the way it's worded I can see why people might misunderstand though.