"Wouldn't this kill any mold in the bottles?"
Yea it's dead, but most people really don't want to drink chunks in their beer.. soup maybe, but there isn't a market for chunky beer.
Harry your method is fine as you are doing it prior to bottling. It's just remember to visually inspect if you have doubts. Pull any that need it out for extra cleaning. Also consider if you haven't already doing like 60 bottles for a 5 gallon batch. That should leave you about 5-6 bottles to plug in if something sneeks through all that washing.
Consider using a flashlight or hold bottles up to a bright light when preping too. Crud will show up in bright light. Think of it as "candeling eggs", cause even sanitized crud is still crud.