This term appears to refer to a key section of a building ("wichtiger Auftaktbaustein", etc.). In some cases, a "Gebäudekopf" denotes an "end section" of a complex, as seen in this text on the ARD studios in Berlin:

"Am Reichstagufer wird der Übergang vom alten ***Gebäudekopf*** zur neuen Bebauung durch einen niedrigeren Bauteil – das Wohngebäude – als Zäsur deutlich ausformuliert, alter und neuer Kopfbau in der Wilhelmstraße haben identische Höhe und bilden so ein großes Tor; die Einfahrt in den gemeinsamen Hof."
http://www.susa-verlag.de/pdf/ard.pdf

The word "Gebäudekopf" seems to have been invented by German architects - at least that's what my wife - who is a German architect! - says. In your text, the role of this "Gebäudekopf" is clearly explained. I wouldn't get too hung up on finding an exact term in English. Just describe the situation in your own words - an architecturally impressive older structure has been incorporated into a new complex where it plays a key role (perhaps as an entrance?), but is not necessarily the "main building". After writing "key section of the complex" once, you can refer to this as a "section" thereafter to avoid making the text too wordy.

Hope that helps.