OK here's the skinny on wearing booties over your stocking foot waders.
1) first of all it is to provide some kind of sole for your feet when you are not in the water. Most of us have spent our whole lives in shoes and those times when we don't have a sole over our feet can be painful!
2) they protect your feet and wader stocking feet from puncture and abrasion.
3) they add a layer of protection for your feet from your swim fins at the points of contact. Blister savers!
Here is the problem though, and I am glad you mentioned surf fishing because this situation is a special problem for wearing booties, over waders. Most fresh water fly fisherman are familiar with gravel guards. Gravel guards are essentially an elastic band they wear over the tops of their wading boots where the tops of the boot meet the waders. They are to prevent gravel from getting into your wading shoe between the shoe and your waders, where the gravel and sand becomes trapped and grinds away at your waders. When you wear booties over your stocking foot waders in the surf even with gravel guards on, your boot will fill with sand and begin chewing your waders to bits, usually pulling the welded seams apart. I have ruined many very expensive sets of waders because of this. SO,... I went and bought myself a cheap set of BOOT FOOT breathable waders that are for surf fishing only. Ok ,they are a bit uncomfortable, and clunky, But really, most surf fisherman on this coast rarely wade deeper than their own crotch! There is really no need for it. Besides wading in the surf above that is downright dangerous! Anyways, If you are going to do a lot of surf fishing, ( and by the way Barred surf perch fishing is off the hook right now!) I highly recommend you consider buying a cheap pair of boot foot waders to do it with.
Booties over waders?, Great for tubing or toonin'
Surf fishing? not so much.
just sayin' bodfish