It's a way of putting a beat LED right in the middle of two le MEC boards and in line with the bottom row of buttons. No special holder or bezel is needed, although that would be an alternative. The LED could possibly be soldered directly to le MEC's J5 header, but I fear the legs will be too short. I need to check the final panel spacing to give more info, whether a header should be used to raise it etc.
A common-cathode bicolour 5mm LED is recommended (e.g. Reichelt LED 5 RG-3) or perhaps use an RGB LED and choose two of the colours. This way the “measure” LED function can be assigned to one colour and the “beat” function to the other.
Of course, there's a quote from Thorten Klose on the back, who created the MIDIbox SEQ: