I think it depends on what you want to use the bed for, what items you need to pop in now and again, stuff you leave in all the time etc and how often you want to access them. If you start off with some boards like your picture then you can see what works for you and soon decide if you'd like to change it. Better than investing in expensive stuff and feel it's not very useful.
I tend to bungee cord things which might fly about or are delicate to the side rails. My F150 only had a couple of hooks and no side rails so I added a rope down each side with knotted loops every 6" which was very handy and a cheap way of adding extra anchor points.
I like bedrugs which stops things sliding about and does limit the amount of stuff you have to secure, they are very kind on the knees too.
I'm not a fan of reaching over the side in case of paint damage and certainly wouldn't put heavy or awkward items at the front except if going to get in the bed to take them out the tailgate.
Storage boxes are useful for small items and sit fine on the bedbug without slipping. This time I've ordered Ram boxes so I'll have to see how I get along with those when the Ram arrives, hopefully will be useful and I won't need boxes in the main bed but I do have reservations of accidental paint damage so will be selective about what I put in them.
When I am carrying a lot of tools (plus I often fail to remove waste materials and extra tools at the end of a job) it can take ages to empty everything when I need the full bed space. Discipline is the answer, I always start off OK but it soon just becomes a free for all mess.
If you want to carry long items then a bed extender is a good idea, I was surprised how often I used it when I first had one. I'd wait and see how you get along and decide if you think one would be useful, personally I like something that can be removed right out of the way rather than those turn over sort which splits the bed into two sections when not in use.
For a few bags of shopping or similar clean things I use the cab.