Don't grant Skill points per encounter. TDE is not meant to be Encounter based but Plot based. The use of experience or Skill Points is something for downtime between adventure, something that reflects time spent on reflecting on the adventuring life.
In earlier editions you don't even grant skill points in most editions, you grant experience, which then is used to level up (1-3E) or pay for sills or feats directly (4E). This Experience was no longer based on killing stuff since 3rd Edition, and that is a good thing! There is a saying in Germany about "GM, I need 10 XP, are there rats in town?" which stems from these olden days where adventurers would go and clobber small creatures to level up before going after the adventures. Since the later 3rd edition Experience is granted for story: completing arcs of your planned plot with a possible bonus for achieving objectives, good RP, and encountering something new.
Meting the first Zantim granted some experience if you survived, but for the second Zantim you'd get no extra experience. It doesn't matter if you won or ran away - you only get the 'new experience' experience once, and you hand it out with the plot experience. The whole idea of TDE is plot centric, not encounter centric. Keep the Experience for the pot to keep the players focussed on the plot! Breaking down the handing out of the experience is a task that takes away extra time from the adventuring, and it ultimately saves time to bundle up handing out the whole bundle at the end.
The books for 5th edition suggest the values you quote to keep up a somewhat sane scaling and matching for the playstyle that the published adventures depict. The bigger the adventure, the bigger the payoff. For a good flow, the given values in the book form a good baseline while a series of adventures that are very 'high scale' could warrant a few extra points to get the players a little edge.
If you have to indulge in the travesty of giving rewards per encounter, don't play TDE but D&D.