it doesn't have to be bolted down but it won't hurt to do so.you're going to glue it to the pipe right?why did you remove the flange anyway?was it broken?don't worry about the flange being to low.you'll be fine.also always buy the heavy duty wax ring to be sure.when you set the flange make sure the bolt holes for the toilet are going to line up with the toilet.i do a lot of toilets seals and sometimes i stack a wax ring without the cone on top of the one with a cone if i feel the flange is too low.which in your case it won't be.you can't have too much wax.btw fluidmaster makes a waxless seal that uses o rings to seal the toilet but i've never tried one:yet