CSS rules that the theme gets from a function

It’s a CSS answer rather than a WP answer, but adding !important to your CSS rules should do it.

Anywhere in your child theme’s CSS that you would like a rule like this…

.comment-list .reply a {
    color: teal;
}

… to override the inline CSS then try using this in your stylesheet instead:

.comment-list .reply a {
    color: teal !important;
}

Any rule with !important should override a rule with the same selector in an inline stylesheet.