Answer

Overflow spaces for alien life traces are distinct from the three discovery spaces for the purposes of species discovery. The rulebook specifies:

• "Below each alien board, there are three discovery spaces representing traces of alien life that must be filled to discover the species."
• "Once all three discovery spaces are filled by markers (in a 2- or 3-player game, these may be nonplayer markers) the corresponding alien species is discovered."
• "The area below the 3 discovery spaces is for extra alien traces. Sometimes you get to mark a trace, but all of the spaces for that color have already been taken. If that happens, you can always place your marker in one of the species' overflow spaces and score 3 points."
• "If a card refers to a trace marked for an alien species, all markers in the overflow space count, as do any markers on the discovery spaces. (The markers on the actual alien species board count, too, of course.)"

From this, it is clear that:

• Only the three discovery spaces are relevant for species discovery—once these are filled, the species is discovered.
• Overflow spaces are for extra traces and are used for scoring (3 points per marker) and for card effects that refer to traces marked for an alien species.
• Overflow spaces do not contribute to the discovery of the species; they are only used when the discovery spaces are already full.

Source: page 20

Summary

Overflow spaces are not used for species discovery; they are only for scoring and card effects. Only the three discovery spaces count for discovering an alien species.

Source: Core Rulebook (pp. 11, 20, 26, 28, 3)