I could not find any relevant information on this, but I find it hard to swallow that it\'s not doable.
How can I customise the arrow for the popovers? I already did
For anyone using a custom style.css to simply overwrite bootstrap without recompiling the LESS, the css rule you're looking for is .popover.top > .arrow:after { border-top-color: yourColorHere; } to change the color of just the arrow.
.popover.top > .arrow:after { border-top-color: yourColorHere; }