what stops my guild from getting 20 players, flagging up for a faction and doing a run by rolling as a blob through those clusters?
A short run on an ox with a large package is like 7 minute in one direction, so <15 minutes for the full run if you use the shortest way.
You can take a little more time and go somewhat around most obvious killzones, and that still leaves you with 3 runs per hour.
Guilds can do that a few times a week. If they really zerg up, like >20 players blobs per blob - or just do alliance-runs with >60 players - they can generate over 500 essences per hour.
For the biggest alliances like ALONE,POOPS SQUAD,TRUTH this may hold true if they realy organise well. It will be mess tho cordinating whole alliances to flag as only specific faction.
There is on other hand the possibility to mass 400 man on oxes and zone cap the maps but this is another story.