It is not a DefleMask issue, PC-Engine require 32xN writes to change a wavetable N times. This track uses lot of Wave Macros and they are looped, sometimes without reason, so it sends over and over again 32 commands per tick. The VGM is simply storing what the artist is doing with the soundchip.
EDIT: This track is looping the same Macro over and over again for 2 instruments, the VGM should be of 600kb without the redundant loops.
I updated DefleMask, because I added a check that will avoid to rewrite the same Wave more than 1 time. Please re-download DefleMask. And Chip Champion, please re-upload that 4mb VGM file and replace it with the new output VGM or remove the redundant loops of the instruments, the file should be of ~600kb !!!!!.