a bit confused at just whether there is an issue with the system, or an issue with how it is being compared.
You are comparing the slower xp rate of killing mobs versus the accelerated xp rate of crafting--not a fair comparison. Also, you are comparing how the rested bonus is showing in the TNL space of different XP bars for different jobs/levels, so it may be a little misleading visually as well.
For example, I logged out last night as an 18 CNJ, close to 19 (just need to finish one of the last 2 objectives on it's hunt list to ding 19). My rested XP was rolling over on that job, so it was the light blue bar. I changed to my 17 ALC, which had just dinged 17, and my rested xp was extended as a bronze bar to about 2/3 or so of the xp bar. I made 4 Ethers, and synthed 38 cloves into oils, and there was still a sliver of my rested xp left. Bear in mind, that I was getting upwards of 1100 xp PER SYNTH--when I got quality past 20%, it would sometimes hit 1800+.
Yes, I burned it down in a matter of minutes vs. closer to an hour smacking mobs....but I was burning it at 4 or 5 times the amount of return per event that rewarded XP. If you are getting 1000/synth it will take considerably fewer events to burn say... 20k of bonus xp versus doing it at 300/kill out in the field. Couple that with how long it takes to synth 20 items versus soloing 67 mobs capable of maintaining 300 xp/kill on average, and you can see that one will most likely take longer than the other.
[Edit:]
Note also that your bonus applies to xp earned just for your actions. It doesn't apply to rewards from FATES/quests, only from the xp you get from killing each mob. With crafting, that is all you are earning XP on (unless it's your first synth in the log or crafting for a quest and getting a reward there)--so you may well be seeing it burn down in a much more focused manner when crafting vs out in the field where you get small xp/kill rewards and big bonuses from content like hunt logs and FATES. For example... level 10 bombs out in the summer event FATE that yield like 50-70 xp/kill and then you get a few thousand XP when it ends. You can earn that much xp from just a few synths.