I should imagine most implementations would be using custom colors instead of the six presets available to choose from. However, when using custom colors, we get 354 lines of CSS rendered in the head for every page request meaning there's no caching or bundling support available which is a significant limitation.
I've tried to copy the generated css and place it in a file of its own but there's no way of preventing the custom css from still being generated.
I would appreciate any help in resolving this issue or perhaps it might be possible to add the option of disabling css generation in a future release.
I understand that it is not a recommended way of adding css, but we have implemented it in that way because of the multi-store support. We wanted to avoid generating a css file for each store in case of a multi-store scenario and that is way we have done it that way. You can get rid of the generated css by choosing the default color scheme (the first option in the administration) and save it. Then no additional css will be generated. You will just need to use your custom css file with your colors.
Note: you should check that you have the following settings present:
value: f74258, 00a1b1
If it is missing, just add it from All Settings admin menu, clear your cache and then save the first default color scheme from the administration of the theme.