Not sure if this applies, but something to try.
In the Applications folder, find the folder for FileMaker Pro/FileMaker Pro Advanced and open it. On the application "FileMaker Pro Advanced.app" bring up Get Info. Toward the bottom of the General section there is checkbox "Open in Low Resolution". Restart FileMaker and see if that does the trick.
For me, it behaves just fine. Exactly as you would expect on a retina display. It is not scaled down. I think if you mess with the resolution setting on your monitor, or install something like Display Menu to unlock non-standard resolutions, you may experience different results. But at the standard resolution, it is just fine. Just make sure that any graphics you use are 2x their "normal" resolution, or they may look soft. Native FileMaker elements show up just fine.
That is what I was looking to hear. Thanks.