Unless the toilet is shimmed up that high, it will create problems. Disregarding that, I can't think of a good reason why any competant plumber would do that - the toilet should be sitting flat on the floor; it might need a minor shim to keep it from rocking, but 3/8" of caulk around it is not right.
Make sure that the valve is opened all of the way. If it is, then try closing it a little. He may have bent the pipe out of the original position pulling the compression ferrule off, and now it is hitting on things. Again, not very good craftsmanship in my unprofessional opinion. If there is some play in the valve, try pushing it back a little (probably won't help since the pipes, once bent, don't like to bend back). But, if while holding it back, flush the toilet and see if that stops the noise. In fact, prior to that, watch the stop and see if it bounces when the toilet shuts off.
Did he replace the flush valve, too? Some brands are more prone to water hammer than others. Korky QuietFill and the Fluidmaster 400a both seem to be pretty good about minimizing water hammer.