The login page logo can be managed by CSS as well as the System Preferences. The attached style.css is the base style and the dark_theme.css overrides it. Any custom themes will be based on the style.css file, like dark_theme.css.
What you would to do have different logos attached to different css themes is this:
First, hide the logo image
#header-logo img {
display:none;
}
Then you set the background of the header-logo object to your custom image
#header-logo {
width: 216px;
height: 65px;
background: url('/images/uploads/custom-logo.png');
background-size: 216px 65px;
background-repeat: no-repeat;
}