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masp - it would seem that different icon display sizing algorithms are used for the Yes/No (and checkmarking) icons and column icons. Maybe because a column icon can be displayed along side its text, or within a composed set (array) of icons, or maybe because it just is
You could do as DaltonST suggests and edit the green tick and red cross icons to have a transparent frame before you add them to cc-icons, or you could find some alternative icons. I'd do the latter so as to clearly distinguish my column icons from calibre's Yes/No icons.
BR