How about just putting a hole down the center of the highlighter for a replaceable ballpoint pen unit?
Basically, it's a clicky ballpoint pen with a highlighter marker surrounding the pen unit. Click the pen forward, and it's a pen. Retract the pen, and it's a highlighter.
This pen looks and acts
like a conventional clicky pen. However, the front of the pen is a removeable cap; the cap conceals a coaxial highlighter marker around the central pen unit.
With the cap removed, clicking the mechanism switches the device between pen mode and highlighter mode.
This cap has a central hole. When fixed to the front, this hole allows the pen to poke through. When fixed to the rear, this hole allows the clicky push-button to poke through.
[edit: original description added]