Vinyl floor at toilet flange sealing question (photo attached)

Photo attached...............................

Hi,
I just replaced my vinyl flooring, and miscut at the toilet flange. I don't want water to get under the floor again, is this type of cut typical? Do I need to seal it with silicone or something? Thought a plumber would know, since you guys see toilet flanges more often than I do.
One other problem (and I have read about options, none are fun), the toilet barely touches the floor (cast iron flange) and sits on the flange, the bottom of the flange lacks 1-8 to 1/4" to touching the floor (and it has two layers of sheet and 1/4" luan, still not quite enough). There seems to be a lowered area in the flange (where the lead is) that would hold enough wax to likely seal, but wanted to get opinions on a good fix. Shims, or plastic base? I have seen a base by Oatey, but no one around my area carries it. (One tiolet, have to get it back in service in a few hours). Thanks a lot, I appreciate any advice.
Tom

Dont worry about sealing the vinyl to the flange.

Use wax without horn,
You may need to shim if the bowl is riding high.
I like plastic door shims, I get them in the door department, not plumbing.
The door shims are about 6" long.
Then caulk around the base.

Thanks. I was just concerned about the exposed plywood, don't want to replace it again. So the exposed wood is ok, or better to coat it with caulk or paint?
I just measured the flange top surface is 3/4" from the floor on one side, and 5/8" from the floor on the other. Will this seal ok? I will try the shims you mentioned also. Was considering a sheet of 1/4" wood or plastic under the entire toilet, but not sure if it would be a good idea. Again, trying to avoid rot.
Thanks very much for your help, I appreciate it a lot! We have one bathroom, so it's urgent. Thanks again.
Tom

just measured the flange top surface is 3/4" from the floor on one side, and 5/8" from the floor on the other.

Click to expand...

That's pretty darn high.
It's going to be a problem.
You may want to make a marble platform to place under the bowl.

All flanges are designed to sit flat on the finished floor with no gap under them. ANy toilet should fit if it is installed that way. If it is high, and especially with a cast iron flange (which is thicker), then many toilets will have problems.