Brandon, I am sure Greg will answer but the reason they are trained together is they are competed together. This is primarily an O/Lift program so the program trains as if you were a competitive lifter who doesn't want to lose all semblance of GPP. That is also the reason that we train snatch then clean and jerk as that is the order of the lifts in competition.
We should be going into an active recovery week next week followed by 4 weeks of a strength cycle.
If you can I would highly reccomend using the CA WOD's just as they are written for the next 9 weeks to see how you like the layout. I have followed them exclusively since inception and have seen the most improvement ever with my lifting. The improvements have come not just in the snatch and clean and jerk. In December I set something like 7 new PR's; SN 142, C&J 187, FS 225, Press 125, Helen 12:30ish, Dead Hang P/U's in a row 13 and there was something else but I can't remember off the top of my head. For my Snatch that is a 32 LB improvement since I began doing the CA WOD in October.
I have toyed with the idea adding some DL's or different lifts. Everytime I start to think like that I remember one of Dan John's quotes. "You can't be your own coach". He also says if you take someones program and change it you aren't doing the program anymore.
In summary it's a great program if you can give it a try.
What we think, or what we know, or what we believe, is in the end, of little consequence. The only thing of consequence is what we do. -John Ruskin