Correct me if I'm wrong, but isn't the text in the manufacturers flight handbook a manufacturer reccomendation?
In the US, ATC is advised with the following:
9-4-4. SEPARATION MINIMA
Separate known aircraft from the aircraft dumping fuel as follows:
a. IFR aircraft by one of the following:
1. 1,000 feet above it; or in accordance with para 4-5-1, Vertical Separation Minima, whichever is greater.
2. 2,000 feet below it.
3. 5 miles radar.
4. 5 miles laterally.
b. VFR radar-identified aircraft by 5 miles and in accordance with para 5-6-1, Application.
As far as thunderstorms are concerned, if you want to fly through/near the stuff that makes St. Elmo go nuts on the windscreen and (occaisionally) leading edges while trailing a plume of kerosene, go for it.
If you want me to dig out Boeings research data, I can only point you to;
AERO - Overweight Landing
Their Flight Handbooks
There used to be another PDF file on their site which I had a link to in the past, but since they redesigned it I haven't been able to find it (actually still comes up in a google search but now goes to an error page). If I find it I'll be more than glad to pass it on to you.