Mm, how to explain...
First of all, yes, it should be running at 60fps. If you notice anything that indicates otherwise or any slowdown at release please tell me and I'll look into it as best I can.
As for the display stuff, let's see...
By default, the games are set up to maintain the aspect ratio. In fullscreen this means that it will automatically create black bars as necessary to fit the aspect ratio at that resolution. Automatic letterboxing or pillarboxing. Chronicles mode is not quite 16:9, so even with that you'll get some VERY slight pillarboxing, since PSPs are also not quite 16:9 and that's of course what Chronicles mode was based on.
In windowed mode, it means that it will a window of the nearest correct-aspect size compare to what you have specified, and when you resize the window manually, it will resize both ways to make sure the aspect ratio is still maintained.
If you want the games stretched out to meet the specified resolutions instead, you can untick the aspect ratio option and it will do exactly that. This will disable all automatic letterboxing/pillarboxing, and will disable all windowed aspect ratio correction.
There is no truly native 16:9 or 16:10 mode at current, but I'm planning to look into it post-release. The thing is, due to how the games work internally, I absolutely can't make any promises this time. I am looking at my options because I'd really like to have an adaptable widescreen mode like what Oath and Origin have.
Personally I think it's just fine using letterboxing/pillarboxing for whatever screen mode you'd like to use in fullscreen, but stretching is there if you think that'll suit you better. The two different screen modes (Complete which is 4:3 and Chronicles which is at least VERY CLOSE to 16:9) will at least give you more options for less boxing or stretching on different aspect ratios.
In summary... you'll only truly be playing on a rectangle in the middle if you use Complete mode and maintain the aspect instead of stretching. I'd suggest using Chronicles mode for 16:9 if you want to almost fill the screen without stretching.