It was my understanding that the beacons were supposed to supplement the alpha NPC's, but then they reduced beacons drops too; did they remove the spawns that dropped beacons on alpha as well?

This looks alot like a series of changes were the devs lost track of the line of reasoning behind them.

Beacons provide the exact experience that is being asked for here; A predictable level of challenge with appropriate rewards.

The beacons also serve the devs purpose, of not having infinitly farmable spawns on alpha were vets can print NIC.

The solution to the alpha issues lies in revisiting the 'beacon style' of NPC farming.

Add in a new artifact category, similar to infestations, but perform exactly like beacons; including possible escalations.

Make beacons available again on the lower level static spawns. This gives players a reason to farm them, something mid-level pve players can do solo or in a small group, then the large group can gather at a convient time to do the more difficult beacons.

Add in real group daily missions, that trigger beacon type waves for players with the reputation to unlock them.

Combined, those (3) things will bring alpha PVE back to an interesting level, and provide plenty of daily farming without creating NIC farms.