As one who lives pretty much underneath this point, and so observes things from the ground, I have a bit of an interest.
It's not only the LCY departures that have bust their level here; the last AAIB report I recall at the same point, it was the Heathrow arrival which had descended below their assigned level.
Don't think that going up at 3,300 fpm out of LCY is somehow necessary for obstacle clearance, there are plenty of F50s climbing much more sedately out of LCY which comply with the limits perfectly well.
I wonder why inbound Heathrows are sometimes descended to 4,000 feet at this exact point; again from observation they pass overhead at a range of heights, and why an extra 1,000 feet as a buffer cannot be allowed at this point I will leave for others to comment on. Certainly on the odd occasions when LCY is on easterlies and Heathrow is on westerlies, inbounds to LCY are turning finals over the Houses of Parliament at 3,000 feet, and the Heathrow inbound traffic is obviously all still at 4,000 or more, so quite why they have to be down to 4,000 some 6 miles to the east is something I would be interested to know the reason for.
Did I miss in the report that the LCY ATIS also emphasises the 3,000 feet limitation, or did this not get put on until after this incident ?