Put the rod holder up front of you. It seems most have a holder there and my line never seems to get wrapped up in it. The only thing my line constantly gets caught on is my paddle leash. You would think I'd have changed it by now.
I made a "holder" on the side of my yak that allowed me to lay the rods along side the yak and then I could bungee and use the paddle holder to secure the rods to the boat and it works well. However, that means more water in the reels. I now need a new fly reel.
I think if I had a scrambler, I think I would just lay the rod in the boat between my legs and maybe run some bungees across to insure they stayed with the boat in case you go over.
the other though I had was if you don't plan on trolling with the rods, then why use the rod holders? Just get yourself a milk crate, attach some pvc and cut out a slot for the reel to slid into. Then bungee crate to yak.
whatever you do DON'T mount them where you have them in your picture. You will be banging your elbows and arms on them not only when you are trying to cast from the boat but when you paddle as well. All I do is flyfish out my yaks and I have a single scott rodholder mounted front and center. Nothing ever gets snagged on it or hits it, etc. When you are actively fishing just pop it out and lay it in your tankwell or something if you feel it interferes with some of your retrieves.
Unless you are bringing spinning outfits I don't see the need for multiple rodholders. Plus if you want to do that just get a milkcrate and mount 2-3 holders across one of the sides of the crate which you can take in and out.
As for launching from the surf to fully protect your rods you are going to have to have them lay along the side or inside where they will not impact anything if you get flipped. or you can put them in a rod/reel case, strap that in and just assemple the rod once past the breakers, it really is not hard and then your rod is fully protected.
Make sure you sit in your kayak in your yard and even cast from it as well as make paddle strokes to ensure nothing you are mounting is in the way. Once you start drilling holes it's too late to go back if you find out afterwards that the location is wrong.
I like to keep my stuff very simple. I find it much easier that way. I don't want or put 100lbs of gear on mine for flyfishing. You just don't need it. If you are trolling or conventional tackel fishing then you might want all of that but I don't use mine that way.
It helps to look at other kayaks that experienced folks are using and even see if they will let you try it out to know what you really like and before you start drilling a bunch of holes.