I haven't read the paper and wonder how accurate the I.T. description might be .
The "as" in "Newgrange’s real significance as an Iron Age “Hiberno-Roman cult site” (not a direct quote from the Gibbons , but from the I.T. ) doesn't suggest a detraction from the real significance of the monument .

That there might be a problem with the light box may well be perfectly valid , it would be good to see the argumnet .
Even without the " roof box ", the passage is still oriented towards the winter solstcice sunrise and it would be difficult to argue against the intentionality of that alignment . The orientation was not an O' Kelly construct .
I was unaware of the Chris Scarre nomination of one of the "worst archaeological reconstructions 2006 " gong , but that is more than likely due to the facade and nothing to do with the orientation of the passge .

Nice blog from Ken on this:

https://blog.shadowsandstone.com/2016/12/27/raising-the-roof-comments-on-the-recent-newgrange-roofbox-controversy/