The custom_icon_theme.rcc file is not a perpetually up-to-date file. Since you uploaded this file to your computer, Sigil has changed, and new icons have been added, so the file must change and should always be based on the latest "base", i.e. the file from the last release.
You don't see the icons in the F&R panel as a side effect – you don't have those icons in the RCC file, so Sigil displays the text instead.
Creating your own new custom_icon_theme.rcc file is not very difficult, but it's about consistency.
If the icons under the Preview window were to be monochrome, then two of them (copy and print) would also be monochrome in the "File" and "Edit" menus, respectively.
Perhaps you want all icons to be monochrome, then the problem does not exist, because you can easily prepare icons in the Material theme with a selected or even any color (slightly modifying the Python program).
This is described here:
https://github.com/Sigil-Ebook/IconThemes
And the answer to your last question – unfortunately, it is impossible to change the color of the icons to monochrome only through the qt_styles.qss file.