Sorry, that reference should be page 14, it's just after the wake turbulence stuff. The 5000 feet is only for unknown traffic, for known traffic you can use 1000' vertical.
For ATS surveillance system (we used to be able to call that radar) separation between known traffic this will be specified in the MATS Part 2. In our case it is 3nm between identified targets or 5nm otherwise (note that unidentified and unknown are not the same - confusingly!).
Special VFR is done differently at different units and I can't comment on Heathrow (I don't work anywhere near). At my unit we can use "deemed separations" where SVFR aircraft operating in certain areas under certain conditions are separated from IFR aircraft operating in other areas. Most units will have some sort of "deemer" like this I would think.