So what did the planning report (for the approved house) say about the settlement boundary?
I'm not directly familiar with Anglesey planning so I am talking more generally here but I would say the planning landscape has certainly changed since 1999. In 1999 the planning process was a mystery to most people. These days everyones an expert. Information is more freely available, planners are more accountable, people are more litigeous, etc. etc. There are groups of people who set the planning portal to inform them when a planning application is submitted in x, y or z area. So the moment you apply they are on to you. Nothing gets past the public these days.
So it is possible the LPA did buck the plan in 1999 but if they do it now I'll buy you a pallett of straw bales.