Doing Lair straight through is rarely correct. Lair encompasses a large difficulty range. It is usually better to intersperse a floor of Orc and Dungeon. This is especially true of Lair:6, particularly its vaults. The same is true of Orc:2's vaults.
This is a trap designed to kill the lazy linear player with tunnel vision. Avoid it by maintaining strategic awareness.
There are no bonus points for completing a branch's floors in batch. At most there's a small piety, turn count and ration saving from reduced transit. This probably vanishes compared to the benefits of a smoother difficulty curve: less recovery time, consumable savings, etc.
The difficulty of a Lair:5 or D:12 or Orc:1 varies by random floor generation, unique spawns, player build, gear etc. It is a strategic principle, therefore, to recon branches for exploitable weaknesses. Any time one rests to recover more than 1/2 HP, one should consider traveling to a different branch in search of an easier path.
If nothing else, this gives monsters on visited but uncleared floors time to disperse to a more uniform density.