if i understand your question, changing starting changes is just one value for the models.
All of your models are in
xlights_rgbeffects.xml
# strings
#nodes
#folds
#starting channels
display as [megatree,arches,matrix,.etc]
Your sequences have three files, Example wizards of winter might be
wizards.xseq
wizards.xml
wizards.mp3 (or wizards.mp4 if you are diving with a movie)
Of these three, wizards.xml is the KEY file. It stores all answers to the grid (timing, effects, morphs, fades, colors , .etc.)
You can change anything about a model and it doesnt effect your sequence file (wizards.xml). Make your megtree twice as large. change it from 360 to 180 degrees, change starting channel. This is what is so nice about Matt Brown's architecture sequence is separated from the models. This is why it is so easy to share sequences with another person.