From my own reading around I think the answer to this comes down to the lack of a standardised user interface toolkit and framework across all Linux distributions. These are libraries that developers use to design graphical interfaces. There are several currently, the most prominent are GTK and Qt. Whereas Windows and Mac OS each have their own standardised UI toolkit.
From my testing, bookmark folders appear grey in Google Chrome and Bave browsers in both Ubuntu MATE (GTK toolkit) and in Manjaro-KDE (Qt toolkit).
It seems that Chromium browsers are providing less support these days for GTK due to the rising popularity of Qt in more popular Linux distros. Perhaps Chromium developers have settled on browser user interface choices around the appearance of bookmark folders that just work on all Linux distros at the expense of enabling them to appear yellow.
It might require too much coding effort and maintenace to give the same UI experience accross all Linux distros. For instance I don't think the bookmark folder icons are image files such as .png but are actually svg generated so it may not be as straightforward as the Chromium browser taking an icon from the host distros currently in-use theme set.
Some more discussion here on the Ubuntu MATE forum.
I welcome any further clarification or correction on this matter.
