the term ‘the player controlling Mersa’ means the faction that controls Map 4, right?
Yes this is correct.
You can get Supply Points for Ports only on a map you have your Control Marker in.
On the Strategic Display on the Turn & Terrain effect cards you can see all the points totalled (Map + Ports) for a map you entirely control.
On a Contested map, both players can get the Supply Points for the Ports they Control.
Map 3 is contested. The British Hold Tobruk and Bardia, the Germans hold Derna.
British Total = 4 (Map 3) + 2 (Tobruk) + 1 (Bardia) = 7 Points
German Total = 3 (Map 3) + 1 (Derna) = 4 Points.
Suppose that Map 3 is controlled buy the Germans, but Tobruk is British.
German Total = 3 (Map 3) + + 1 (Derna) + 1 (Bardia) = 5 Points
British Total = 5 (Map 4) + 1 (Bardia) = 6 points.
Note here that Tobruk does not Score for the British because their control marker is on Map 4.