Border cropping is an option by default from the commandline arguments:I hope at some point they're able to add and improve new filters into the actual Display option on the home screen. I'd love to be able to use the CRT Filter and 4:3 modes but the first one is far to heavy handed effect for me and I just can't cope with the warping that you get in the 4:3 mode. That means I'm stuck in Pixel Perfect mode at the moment and although it's not terrible, I can't help but be aware of the aspect ration being wrong while I play games.
I'd really like there to be an option to fix the warping in the expected overman areas in some games. It's really noticeable in games like the Super Mario games and it would be a fantastic improvement for that to be dealt with, even if it was simply a black border that's placed on top of the game.
For example: "--guest-overscan-dimensions 0,0,9,3"
As for aspect ratio, there's the only two options that could possibly be considered "correct", and they're builtin, in either 4:3 or the Pixel Perfect mode. You can tweak any filters you like for any mode in Retroarch.