I think a 9' x 11' foot table is much too large to expect to be able to be able to flip it on it's side for storage. Short of using a block and tackle or some type of hoist system.
I'm also curious why you need such a large outfeed table. You'd have to be ripping stock 20 ft or longer to need that much outfeed table. or perhaps dealing with very flimsy stock that can't be allowed to hang off the back of the outfeed.
While torsion boxes are much lighter than the equivalent solid table, in your case that would be in comparison to a 3" MDF table. A 9' x 11' 3" solid MDF would weigh about 1,100 lbs. With 99 sq-ft of table, at 1.15 lbs/sq-ft of 1/.4" MDF, the skins would be 114 lbs each, 228 total. I come up with 128 sq-ft of webs (what I think you are calling the core). That's another 147 lbs for a total of 375 lbs. Not sure about the hardboard weight, but I'm not seeing how you are coming up with 565 lbs. Maybe I'm misunderstanding your construction.
I assume the flatness and rigidity you want is for the CNC operations. Because generally you wouldn't need that for an outfeed table.
Regardless of weight, I too would look at making it in sections. If you build flat sections, you should have little trouble lining them up.
As to this flatness, it will be very hard to make a table that large that flat unless you already have a very large flat reference. Keep in mind a concrete slab is no where near flat. So you'd have to got to a lot of work to create that surface. Much easier to create a smaller flat surface. Build the first section, then it becomes the reference surface for the remaining sections.
I also would not remove 2" holes from the webs. If the table is 3" with 1/4" skins on each side, the webs are 2.5" tall, and you'd only leave 1/4" in the middle of each side.
I would never put holes that large in the skin. The strength of a torsion box comes from the skins. Removing that much material would reduce the strength substantially. I think it would be close to the point that it would hardly function as a torsion box anymore, no matter what the material, and with MDF, I think it might concentrate so much stress that the material could fail.
And by my rough count that's something like 3,600 holes in skins and webs. That only saves about 78 sq-ft of 1/4" MDF for a weight savings of about 90 lbs. Which is 24% of my weight estimate. Not insignificant, but it's not really going to make it so much lighter. And 3,600 holes!
MDF is great material for a torsion box becasue it is very flat and it is plenty strong enough unless you plan to beat on it with mallets and hammers. But it is a bit heavy. Plywood will be about 2/3 the weight, but won't be as flat. But still possible flat enough.
I also second Rick's suggestion that you look at the Ron Paulk table design. It is specifically designed to break down. Though his design I believe is 2'x8' sections, but can of course be modified to whatever dimensions suit the need.
I'm not sure what you are doing with the CNC, I know a guy that has a 6'x10' or so professional CNC bed. The top appears to be particle board. It is solid with no holes. No idea what the frameworks is. But it must form the top of some sort of box. He hooks up a vacuum to it, and it draws vacuum through the top surface. Apparently the particle board (or whatever) is porous enough. He can lay a sheet of material on this, turn on the vacuum and that sheet will not budge.
As long as the parts he is cutting are not too small, he doesn't need to hold the material down in any other way. Not sure if that might apply to your situation, but something to consider.
One other comment on torsion boxes. There's a lot of misunderstanding about how these work and many people go to a lot more work than needed. The internal webs or core serve one purpose, and that is to hold the skins apart at an equal distance. The webs do NOT need to join to each other. This doesn't add strength. The webs do NOT need to be continuous. They could just as well be random lengths placed randomly around.
Again, they only serve to hold the skins apart. The important joint in a torsion box is the bond between the web and the skin. This needs to be strong. Fortunately this joint is in shear which is where a glue joint is strongest.