Maybe it's just me, but I think this is reasonably clear.
All the way through it is stated that Paalm has only one spike and Harmony can take control when a second spike is introduced. This is exactly what we see happen - new spike: Harmony starts to take over.
The confusion over whether the Trellium spike is an extra seems to arise from Marasi's line in the epilogue "That's one of the spikes she was using."
This seems to imply that there was more than one spike. However, we also have this from Marasi slightly later: "It certainly wasn't one of the spikes she started with. That means she removed both, and stuck one like this in instead."
So that's one spike total, not one plus a Trellium one. Marasi continues: "Where did she get them? Who gave them to her?" (emphasis mine)
Clearly, according to Marasi, there is more than one Trellium spike. Otherwise she would say "where did she get it?"
MeLaan explains in more detail later on: "She used these strange spikes to steal attributes, instead of the ones we're familiar with. Maybe that's why she could use stolen Allomancy and Feruchemy."
So there were multiple Trellium spikes, which she used to take powers and used one at a time. Surely if she could have used more than one at once, she would have done so.
As Marasi says, she removed both Blessings and replaced them with a single Trellium spike. She then powered up several Trellium spikes and switched them in and out as Harmony described, not using more than one at once.
At least that's my understanding of it.
Cheers,
LJ.