There isn't much allowance for raised flanges in most US toilets I've seen. The critical feature is how much higher the under toilet "ceiling" is than the bottom perimeter base that sits on the finished floor. Since this dimension is intended to work with a standard wax ring, there's little chance a 3/4" protrusion will work. Not only do you need physical clearance between the flange and the "ceiling", there also must be room for the wax sealing ring.
The other potential conflict is the outlet horn and how it fits into the small bevel of the flange fitting. Again, there needs to be room for the wax to fill this gap. You do not want any direct physical contact between the flange and horn.
Simply supporting the flange is not enough. The perimeter base must be fully supported. If you try to install the toilet as things are, the toilet will be balanced on the wax ring. It will wobble every time it is sat upon, eventually forcing all the wax out until the "ceiling" is bearing directly in the flange. While the wobble will diminish at this point, it will still wobble. The seal would obviously be compromised.
Whatever you do, the perimeter base must be solidly supported. The obvious solution is lower the flange, though very difficult in your case. Another solution would be to raise the floor, which I imagine would be undesirable. The only other possible solution would be to raise the support of only the toilet base, such as setting it on a grout bed. Depending on the nature of your flooring and the actual final thickness of the grout, this may not be too bad a solution. You would need to spend enough time finishing the exposed grout around the toilet base so that it is smooth and easy to clean.
It should not be necessary to try to goop some type of sealer around the lower neck of the sink drain. Such solution may work but it is not the desirable approach when you consider that someday this assembly will need to come apart for repairs.
In looking at the assembly that you have I wonder if one or more things are at play here.
1) If the drain pipe tail was not centered in the neck of the sink drain and then had lateral force on it due to the down stream goose neck trap it could be forcing the gasket open on one side. Check that there is no undue large amount of sideways pressure on the lower part of this pipe assembly.
2) It looks like the gasket directly contacts with the face of the capture nut around the drain pipe. It is possible that by tightening the capture nut that it is putting a twisting force on the gasket that may cause it to "fold away" from the sealing edge of the sink neck.
3) It is possible that there could be a small crack or pitted area on the sink neck that keeps the rubber gasket from engaging 100% with the sink neck.
4) Sometimes the "rubber" used in this type gasket is made of a plastic material that is anything but rubber. Check at the local hardware store to see if they have another gasket that is more pliable. In some cases a silicon material may be better.
Best Answer
The flange coming out of the disposer secures the pipe that attaches to the drain. There is supposed to be a rubber washer behind the flange that when the flange bolts are tightened seals the pipe connection from leaks.
disassemble once more and verify there is a washer behind the flange. If not get one and skip the putty.
If the leak is from the sink basket where the disposer attaches at the sink bottom it may be due to:
-not enough fresh putty. The putty should be rolled to a 3/8-1/2 inch diameter and overlapped where 2 pieces are used. More is better in this case.
-press the basket into place before tightening the screws underneath. You should see putty being forced from under the baskets flange in a continuous ring.
-the sink edge for the basket is bent or damaged. check for burrs or lippage with you finger.
-the basket screws aren't tight enough.