My impression was that they aren't jack hammering to lower the height, rather they need to expose the rebar cage to give the new pour material the necessary bonding and reinforments. I think at least some of the piers are too low in height and they actually need to raise the elevation. (New KCCI info indicates as much, although it sounds like elevations at all piers and ramps at either end are all over the place.)
The other aspect is the anchor bolts and embed plates were mislocated (or missing altogether), so they would need the fresh concrete at the top in order to place those critical elements.
I am in agreement with you that I don't believe the piers were poured 6" too high. If they were 6" too high they would have to cut out all of the rebar in the top of the piers as the finish elevation of the concrete pier would be lower than the existing reinforcing if they just left it in place. The size of reinforcing in those piers also wouldn't allow enough development length by chipping down 18" to install new reinforcing for a 6" lower finish elevation...you'd have to install hundreds of rebar couplers which is crazy to think of.
I have not watched the KCCI video footage to see if there are anchor bolts even installed in the piers but driving by I can't see any sticking up out of the piers.
As of yesterday, they started installing forms at the South pier top.
What is astonishing is the Liq. Damages are $5,000+/day you would think they would work more than 5 days per week and be working on every pier...unless the schedule is such that there is no benefit in having all the pier tops fixed if the bridge girders are no where near ready to be delivered and installed completely.