When you call getPrimaryEffect() on a beacon that has sunlight you will receive the effect being applied; and it will be the level 2 version if set as such in the beacon

When you call getSecondaryEffect() on a beacon that has sunlight, you will receive the second effect applied, or none if the beacon is using a level 2 effect (or is not a 4 layer beacon)

However,

When you call getPrimaryEffect() on a beacon without sunlight, you will receive the first effect that would be applied, but only the level 1 version, even if the beacon is set to use the lvl2, as opposed to the sunlit mechanism.

Similarly, calling getSecondaryEffect() on a beacon without sunlight will always return null, despite any settings in the beacon.

Effectively, when without sunlight the beacon will return as if it had fewer than all four layers (3, as strength I still works when without sunlight). Worth noting however, is that it doesn't return null entirely when without sunlight, showing that access to the beacon's effects should be possible when without sunlight.

In short, when without sunlight the getXeffect() functions return as though the beacons had 3 layers