Yes, that's a good question. You begin by selecting a pre-existing media setting just like one would with any printer. Then, the profile is made. Then, using EMI or via the control panel, you copy that existing media setting, rename it, and change the settings to suit the paper for which the profile was made. At that point, the new profile is coupled with the new custom media setting. Even then, though, you can still override that via the app from which you're printing, if you choose to do so. The only real benefit to having the profile incorporated with the media setting is that your custom media and profile will show up when you select that media setting versus a generic OEM profile as before. Also, your new Custom Media will appear in the media lists of papers. At least, I seen no other benefit at this stage.
You're quite right that the Epson Media Installer is much like the Canon MCT. Indeed, it was likely inspired by that tool and Epson is still creating it on the fly. Today, we ran into a problem with the new version 1.0. It communicates with the printer, allows us to copy an existing media to make a new one, allows us to rename it and modify settings. BUT it will not allow us to save all those adjustments. It's simply dead in the water.
We called Epson tech support for help. The rep had never heard of Epson Media Installer and informed us that Epson does not support third party software. It took repetitive insistence to get across, finally, that the software was made and supplied by Epson. It came with the printer. In short, we got nowhere. So, the fun continues.
Mick