You can use a flange extension made for the purpose and one wax ring, or double up two wax rings, one with a plastic horn on top down into the plain wax ring on the bottom. The wax ring(s) will fill the unlevel void and level out on their own between the flange and the toilet base.
The toilet should be leveled with beveled plastic shims made for the purpose if necessary.
However, THAT isn't your main problem. Installing tile directly onto wood (plywood or planks) will only result in cracked grout and tile due to the shrinking and swelling of the wood.
The tile should have been installed on cement board screwed to the plywood.
You're going to eventually have to rip all the tile out and do it right. When to do that is your call.