One with, one without
I have both, and prefer the cable run inside the top tube. This, on a Trek Madone, provides a "cleaner and neater" installation. Given how much effort Trek put into this frame design, I'm sure they insured the holes are not detracting from strength or longivity. If the little plastic thingies ever break . . . not sure why they wouild, and Trek no longer stocks them, however unlikely that may be, I'll make my own. I'm sure any machine shop could do the same.
bumper