I haven't understand your question....
what I'm saying what's the difference between your neekbooter.dol file and the dol file inside Neek2O Channel?
They both go to emuNand specified by nandcfg.bin.
Oh I rebuilt everything and all works fine with PL3rev3.62.0
BUT I found a serious error in the neek2o code, here you go:
I have 2 Emunands in USB/Nands folder one is called nand1 where all wiiware are and the second pln2o for PL3-neek2o loader.
My Neek2o channel boots me into Nand1 by default (as specified in nandcfg.bin)
I installed neekbooter in pln2o but not Nand1
When I launch a game in neek2o I go to Nand1
When I install Neekbooter in Nand1 - neek2o launcher works.
So I found that only if you have the default Nand (for neek2o channel) with neekbooter, PL3 will work fine - then the Nand doesn't have to be called pln2o
To fix this PL3 should create a nandcfg.bin file specific to pln2o folder
Hope you fix this bug soon