Hi. The second image is more correct. CRT Royale requires a lot of pixels to work on, meaning you need to apply it on high resolution. I’m not entirely familiar with the process you are going through to reach the “border” results, but you should not need to create a transparent border. The reason why borders are “required” for modern games is simple. Back then monitors and tvs were in 4:3 format. Todays monitors are mainly 16:9, meaning they have additional room on the sides. If you display a 4:3 image on such a monitor, then off course it will not fill the sides (unless you tell it to), to not stretch the image.
On a side note to the different note, there are Shader packages which will fill the sides and possible little bit of upper and bottom part of the screen with nice border images, such as the look of a tv or a handheld. This is called a Bezel. If you are interested into, have a look at Mega Bezel Reflection Shader! - Feedback and Updates (which is part of standard RetroArch Shader package already), Koko-aio shader discussions and updates (also part of standard RetroArch Shader package) or alternatives like CyberLab Death To Pixels Shader Preset Packs (scroll a bit to see the bezels) or P3st´s Overlays for Mega Bezel Shader (Arcade,TV´s ,and more) . But be aware that they can be intimating at first and may require some specific settings in order to function correctly.