Correct me if I'm wrong (a very real possibility) but, once you have logged into your Mac with FileVault, you have access to all files. If so, that means anytime the Mac leaves your sight, you need to log out, put it to sleep, or something. Otherwise, your files are at risk. That is cumbersome and less secure for certain situations, unless you are always extremely careful to log out each and every time. That's not even to mention things like key-loggers, etc.
In the case somebody has one or two files (my case exactly) that they want to have secure and the files are seldom (if ever) accessed, then just encrypting those specific files means I don't have to worry about always having to use a password on my computer. The likelihood that my computer gets stolen are slim to none and, even so, it wouldn't really matter except for a couple of files. So, yes, in my case, Filevault is extremely burdensome. I would have to log out any time I left the computer's presence. I leave the thing running 24/7 because it consumes so very little power and I can turn on the display in a heartbeat and go right to work. No need for logging in or inputting a password because the files at risk are not open. Therefore, they are secure.
And, again, the way I read the disk Utility option, you can place those files, as they arrive on your computer, directly into the secured folder. Again, I could be wrong but, if it works that way, it seems the simplest option to completely secure specific files. Or, in my case, where I create the files, I'm pretty certain, I can create them directly in the secured folder. If I am wrong about this, than all bets are off.
Filevault seems complete overkill except in extreme cases where every bit of info on the computer is sensitive. If you need complete and ultimate security (involved in espionage?) and can take no chances then, great, you may need Filevault.