I don't like them either, but I couldn't find a better way to provide the clock in/out feature and still fit in that area of the board. The optional OCXO on the opposite side of the U.FL connectors doesn't help (can't do edge-launch mmcx, for example), and if you move down you would ruin the legend for the user interface connector.

But fair feedback, noted. I can't move the optional OCXO below the enclosure, as that would be taller than the aluminium block itself and require a slot breaking the RF shielding, but maybe I can move the connectors. I'll try and get creative.

Edit, surface-mount MMCX to the rescue? https://i.imgur.com/1GJhJa6.png