I haven't looked into this story's veracity, or the circumstances, but I will say: bombing raids are wildly chaotic and notoriously unpredictable. Even with saturation bombing and area bombing, the behavior of the bombs, of the fires, of the winds, etc., are extremely hard to model, and you get very unintuitive results of individual people or buildings "surviving" (though how "untouched" can vary a lot) despite ruins around them. (You get similar apparent arbitrariness with tornados, nuclear weapons, and other very unpredictable mass destruction events.)

You say that 90% of Berlin was flattened during wwII, which is a good estimate. However, what you are implying is that all of that was attributed to US and UK bombing raids, and that the Luftwaffe HQ was simply missed or not targeted. Although US and UK did flatten a good portion of Berlin, most of it was destroyed by the russians when they invaded. In other words, this statistic is misleading in which it implies that US and UK destroyed any target they wanted to in the city.

Recently, I wrote a response to a similar inquiry. I hope this helps.

I'm not familiar with this question but I recall a story of a cathedral - weren't buildings easily identifiable from the air sometimes left intact as a site guide for bombing raids?

This is a speculation and secondary question:

I've read that Albert Speer--the chief Nazi architect--built some structures with redundant reinforcements purely for the sake of "ruin value". The idea being that in case the Reich was bombed entirely, it'd look more like the remnants of a grand civilization than one easily paved-over by history.

It seems congruent with his writing, but I've never had it verified that he built in such a way.

Do you have a picture of the building after the bombardment?