Yes, the original 2009 proposal for a shorter northern R3 of 2200m showed a T6 sitting slap on top of the M4 spur.
And if they got it right, slap on top of the railway between Airport Junction and Heathrow-1 2 3, but that history now, apparently.
The latest plan I've seen does indeed appear to suggest the A4 Colnbrook Bypass being interrupted by R3 and T6B and the A4 re-routed along the original Bath Road route (through Colnbrook and Poyle) to a roundabout just west of the M25 (by the golf range), then tunnelling under the airport to resurface and join the original A4 at the Hatch Lane junction.
My intepretation is slightly different (if we're looking at the same document "Taking Britain Further" booklet, page 25):the A4 remains the Colnbrook Bypass north of Colnbrook, then joins the old A4 through Poyle industrial estate to the M25 then disappears (tunnel?). It reappears above the airport tunnel entrance junnction (A408).
That features in a number of Heathrow's recent presentation documents, which talk about displaced thresholds of around 700m on the current runways. That would result in aircraft being about 120ft higher at any point on the approach, which would have a fairly minimal effect on noise.
Not a problem, aircraft will be significantly quieter (and cleaner) by the time any new rwy is built, if it ever is.