Paxton's Emporium in a one-per-galaxy building, so it should not be possible to build more than one.  I and others have reported that it is possible to build more than one, but it was not obvious why.  I have been investigating every time it happens in a game I'm playing, and I have finally found a reason and have a save that reproduces it.

The reason it can be built more than once is that the race that first builds it will destroy it later.  Since none now exists in the galaxy, all races now are able to build it again.  Now the problem is why the race destroys it.

In my game it was destroyed so that a Research Center could be built in its place.  The race was building Research Centers around a Computer Core and seems to have decided it was best to get rid of the Emporium that was next to the Computer Core.  The Emporium is not indestructible.

I have a save just before it happens and a video showing it being destroyed and a Research Center being queued up in its place.  The zip file containing these and a Read Me file explaining what to do is available here.

I'm not sure if this is the same reason why one-per-race buildings can be built more than once.  I still think there is a bug in the way these building are tracked.  If a race has a one-per-race building and loses it, all races are considered to have lost theirs, so all races can now build one.  No effort is made to keep track of how many a race has already built.  In a game some time ago I had three Computer Cores in a triangle, giving me a massive research bonus.  I had built one and never lost it, but it kept showing up in my build queue, so I kept building more.  Something similar happens if I do happen to gain, for any reason, a second one-per-race building, then lose one of them.  The game thinks I don't have any and allows me to build another.  This can be repeated as many times as I lose one of them.  I have actually exploited this in a game to get several one-per-race buildings.