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Good luck and post pics when your done
Tile the floor as normal and grout it. Then to reset the toilet get a new re-inforced wax
Water and moisture is the worst enemy of wood flooring. So be careful bamboo may buckle and warp?????
I usually wrap the toilet in an old moving blanket and place it in the tub...try to get all of the water out of the trap before you move it...you can double up the ring as KMS suggests...but we usually reset the flange to the new height...it's more work but then you're all set....if it's a plastic flange go ahead and add the metal flange plate over it for strength..doesn't cost much and will save you a ton of headaches down the road. When I change out a toilet or make a repair on a rental....I add this ring in where possible. Line up the slots and you can screw it to the subfloor for added support.
I've seen people using the plastic toilet bolts (?) why I have no idea...get the brass ones. HandyANDY does a ton of toilet replacements and repairs. Also, make sure you use a braided mesh supply line. We can refer you to some excellent tilers....hope it helps!
A recent repair: http://youtu.be/2Bw4UxQSJzc
On the durability side carbonized bamboo ( the more common darker version) comes in below many
I wrote a bit more about this on my blog.