Basically, if you buy out the scientific player you don't gain the ability to build scientific buildings. Everything new is treated like a scavenger HQ built it no matter what. However, the current buildings on the map that you bought are still scientific buildings, and they still get the bonus.

it then reverts to being treated like scavenger.

You'd think this would be an advantage to scientific, and in some ways it is, but it also makes scientific buyouts more appealing to the non-scinetific players, so people try to kill them off more than the other HQ's

this would be clearer if the scientific faction had unique building graphics

Technically speaking, only scientific buildings are a different type.  This also matters for adjacency.  If you, as a non-scientific, buy out a scientific player and plop a regular farm next to an existing scientific farms, the farms do not get adjacency bonuses.

By the way, is this still true for robotic?  Since they get adjacency bonuses from adjacent resource buildings, is that effectively a third type of buildings and does the adjacency bonus depend on who built them or who owns them?