This is a tough situation. The boulder escarpment is a perfect human-created squirrel habitat. To protect the long-term stability of that escarpment, you likely need to fill all the inter-boulder areas with concrete/mortar. Depending on the extent and size of that feature, getting an estimate from a licensed contractor would not be a bad idea. 

Excluding from the raised beds themselves would normally involve sinking undiggable/unchewable hardware cloth 3' below the perimeter paired with an above-ground fence - probably electrified. An additional layer of protection could be hardware cloth underlining the bed (under the growing medium) itself. Sometimes people attempt a "moat" approach combining a hardware cloth lined trench filled with sharp, coarse rock/gravel. However, your beds are literally adjacent to the colony's burrows, so I'm concerned that their tunnels might (relatively easily) defeat your expensive and labor-intensive exclusion - even if focused on the raised beds - until you reduce the population significantly and reduce the carrying capacity (habitat provided by the escarpment) significantly.
You will not successfully "trap out" the whole population, but your situation is really going to require strong population management (lethal trapping) plus reducing habitat quality (i.e., keeping them from using the escarpment as prime habitat) before you can achieve some efficacy in protecting the high-quality, irrigated plants in the growing beds. That can be DIY for trapping, but also you can consider hiring a wildlife control operator to do gas or gas + trapping to get an initial handle on the situation. Licensed WCOs are listed herehttps://myodfw.com/sites/default/files/2026-06/WPMR101%20-%20WCO%20Public%20Website%20Information_0.pdf 
I suspect you might be dealing with California ground squirrels, which are the largest bodied- ground squirrels we have here in Oregon. (Have you ascertained what species yet? If so, let me know as we might need to adjust some techniques.) The UCalifornia Ag Natural Resources folks have excellent materials that help explain the critically-important seasonality of the squirrels (for baiting, activity vs hibernation, etc.) and also has excellent pictures of trap sets for the (many) trap designs used to control ground squirrels. https://ipm.ucanr.edu/home-and-landscape/ground-squirrel/#MANAGEMENT_52_1
I hope this information helps as a start, and feel free to write back as you learn and explore more. 

Oh boy, thank you for the long note. I am clearly in big trouble with these squirrels. Had I known what they would do I could’ve stopped them a couple of years ago when I first started seeing them. Now it’s at a past the point of no return stage….

If you'll go back to my first reply - I posted a link to ODFW (Oregon Department of Fish and Wildlife agency)'s Wildlife Control Operators - They are licensed and trained to do wildlife control work, such as the trapping and they might (ask them) also be licensed to access poison gas. Gas can be really tricky however - as you can imagine with a rock pile warren with all those access points. Your concern about edible poisons is spot-on - We can't control what eats the poisoned squirrel, and that is a real risk both to scavenging wildlife and also potentially to pets. That's why closing up those inter-boulder areas with concrete and then carefully using lethal traps to reduce the population is going to be vital. The WCOs wouldn't be qualified to do the concrete work - For that, reach out to 2 or 3 local general contractors or concrete/hardscape contractors and get free estimates! 
As for reaching out to experts - You've got that covered - I'm a wildlife professional, and WCOs are trained contractors for these problems!