I'd be cautious dealing with pond professionals. Virtually all build one type of pond over and over. They're likely to try and convince you to build whatever type of pond they build. It's not dishonest, they just think whatever type of pond they build is best and have no experience with the type of pond you want so they rarely can see what you see.
And yes, the standard method is to bring in heavy equipment, scape the site, build whatever type of pond they build and try and re-use some of the rocks. It will look man made, nice, but man made. Natural is more beautiful imo. And of course way, way cheaper.
For sure this would be likely the first time any professional ever tried this kind of setup, working with keeping existing rock in place. IMO you're actually better off doing the work yourself. Pretty easy actually because you don't have to dig much or move big rocks and you keep the beautiful natural look, which like you said, remains valuable if later you want to remove the pond. Screw holes are easy to fill and hide.
If you don't want to screw into the rock you can build a wall instead. You can pound plastic wood stakes into the ground a little (doesn't have to far, a couple inches) right against the rocks, every 12-24" say. The stakes can lean outward and basically lean against the rock. Then shoot your level line and screw the horizontal strips to the stakes. Stake tops can be sawed off flush. This method is tricky as the horizontal board will want to pull inward and something has to be figured out to stop that.
A better option, but one that unfortunately scares many people, is to use rebar. Like 1/2" or larger for the stakes. Thicker = longer it lasts because it will rust at the ground. Then use thin rebar (#2, #3) for the horizontal tied to the vertical using rebar wire. Liner can go over the horizontal and attached to the horizontal after filled with water if needed. If enough liner goes over the horizontal and tucked far enough down the water pressure will be more than enough to keep it in place. The only tricky part is bending the horizontal bar to conform to the rock but it's actually pretty easy to get good at it fast with a bender tool and doesn't take a lot of muscle. Rebar won't want to pull stakes inward and it's generally much easier to pound rebar into even rocky soil so you can get those in deeper. I'd cut the tops of stakes at the level line before adding the horizontal. If a stake gets pounded in too far you can just wire another vertical to it to extend the height to the level line. Wiring the second piece also has the advantage of not requiring cutting the stakes which is tricky, but a little more cost for rebar, but probably less than $20. Thinner rebar can be used for the vertical extenders.
You do have to fill in behind the stakes with soil, concrete, rock to create a surface to back the liner when filled with water, but you have to do this no matter what. I'd use rocks if some are around, or concrete bricks. A little mortar skim coat over the face to finish. Easier to remove than solid concrete later, if needed.
One place a professional might be able to help is someone who makes fake rock. They can match the existing rock and make a little cap to go over liner edge and down below the future water level. That will hide the liner edge and the illusion will be complete even if you don't get the edge perfectly level. Between the rocks soil can be backed filled to the edge and plants can cover the liner there with maybe a little fake rock edging.
Would be gorgeous. I encourage you to try...not as hard as it might seem. Take your time and if some piece isn't perfect just toss it and try again. Look at it as the price of learning and you'll see it as cheap.
