The only khukuri I've made with fullers so far was a three-stage process:
1 - Forge the fullers in with a spring-fullering tool
2 - straighten them with an angle grinder
3 - smooth it out with a 3" wheel on the belt sander
I have a video of them using an angle grinder to put in the fullers at BirGorkha. This leaves little divits in the blades...are you sure you're not mistaking these divits for hammer marks?
Note: that spring-fullering tool shown above would not work to put fullers in a khukuri....that kind is used for fullering a blood groove. This is the kind that you have to use:
Otherwise you won't be able to get the curves in the fuller. Also, notice that the fullers vary in depth from start to finish.
The other option is to use a ball-peen hammer with a fuller hardy:
Lots of room for error either way.....

.....I imagine I'll get good at this after a few dozen more....
I asked JP about fullering and he said that historically they did indeed forge them in (duh...no electricity)...but that as long as there have been grinders around, they've been using those to speed things up.
I'm not saying the fullers aren't forged in....I'm just saying that I asked for a video showing how they made the fullers and they sent one showing them using an angle grinder.