From what they're saying in the "Test" section of the Deploy documentation (http://www.manifoldjs.com/deploy), it seems that it just wraps your website in a WebView?
This is great from a developer perspective, but I'm not sure if the App Store review process would allow doing something like that.
I wondered the same thing when submitting a Cordova app to Apple, which is about 2% wrapping and 98% web site. Just this morning it got through the review process with no problems, so... data point!
That said, we did take pains beforehand to make the "web site" behave like an app: responsive, (mostly) single page, swipe support, and tested across all devices.
My team just got a Cordova app through the apple review process as of yesterday. So, data point #2! I think as long as you try to adhere to Apple's app review guidelines it doesn't matter if you used Cordova or developed natively
You can always go in and edit the Cordova project that ManifoldJS returns and add your own images for icons and such. Not sure if ManifoldJS currently supports this out of the box just yet, though.
Stuffing webpages into a WebView and then selling it on the App Store has been standard fair for years (PhoneGap popularized this method 4+ years ago now).
This is great from a developer perspective, but I'm not sure if the App Store review process would allow doing something like that.