Well I had never looked closely into this feature, and now I found that it generates different colors for each text label assigned. Actually I never used the "Mark books with text label" command - every day, a new serendipity while using Calibre!
The "Mark all books" in the FTS window just sets the matched titles to marked:true, hence the Mark Books submenu item in the screenshot BR uploaded will display the label 'true'. And that's why that tooltip "Marked without text" appears for books marked when using FTS.
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