Your title says B 31.3, but the post says B 31.1. Which is it?
Either way I can't find any reference to a specific code requirement not to bury flanges, but there are many construction specifications or company guidance documents which don't permit this.
If you could provide some reference to the "posts" where this was seen then we might stand a chance of replying better.
Remember - More details = better answers
Also: If you get a response it's polite to respond to it.