Beast Tribe Quest - Reward Discrepancy

Reputation level: Recognized
Sylph issuing NPC: Ponnixia
Quest Rewards:

9315 Exp.
600 Gil
10 Philosophy Tomes
7 Reputation
20 Shards

Reputation level: Recognized
Amaljaa issuing NPC: Narujj Boj
Quest Rewards:

9693 Exp.
660 Gil
10 Philosophy Tomes
7 Reputation
20 Shards

Is this intended? For those at max level the secondary rewards (ie gil, tomes, rep, shards) are one of the primary reasons to do the quests (aside from the rep. rewards).

Have you checked and compared the level of the quests?
The Sylph and Amal'jaa are slightly different level wise...

Sylph quests are at level 42, 45 and 48
Amal'jaa quests are at level 43, 46 and 48

Gil/Exp reward scales by level so what you see is normal behavior.