Mike, do you think that 3 days of CNS would be too much during the General Prep Period?
No. Not if it's set up appropriately. Everything will be relative. What is considered a highly intensive CNS day during GPP might not be considered so much during Comp. phase. Plenty of successful coaches use 3 hard days all year long with no ill effects.
How would this template transition to in-season training?
I'd probably suggest keeping the general distribution of the week the same but just changing the intensities, volumes and methods.
In the first option, what modules do you think conflict or could be rearrange?
It's potentially ok depending on what you do with your weight sessions. I just like to recommend putting all high CNS demand activities on the same days.