Purely from the maintenance aspect, if you've ever heard of Human Factors - splitting a single operator's fleet over two registers and two different Regulation sets is going to prove it does(n't) work.
I suppose they could get away with it if the civil and military sides don't touch, but it will be confusing if/when they do.
If anyone has operated an ETOPS fleet within a non-ETOPS fleet you might know what I mean...