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Yes, with the StoreFront system almost everything is unified into the file system. Everything that you can see under the File Manager tab in the web interface is available to you with FTP. It’s not uncommon for developers to use external development tools to write their code, compile contents with tools like Grunt, and then have it automatically uploaded via FTP.

The current StoreFront template is implemented as a series of velocity templates that provide the same functionality as the single and multi-page checkouts that the existing UltraCart platforms has. The difference being that they are completely responsive. If you’re comfortable with the stock checkout flows then you can get away with minor modifications to the templates. We recommend that you perform the majority of your customization through CSS to make version upgrades easier. If you need a customized checkout flow then you can still use the REST API to build that within the StoreFront just like you have in the catalog system. Future templates that we publish may choose to use the REST API instead of the Velocity templates, but you’ve got to pick and choose your technology battles carefully. For this initial release the best bet what was get a completely responsive checkout experience with Velocity working.

Yes, some themes, such as Trial, use the REST Checkout API to implement the checkout process.  Other themes like Woodland and Fashion use the REST Checkout API to make additional functionality, like the cart snapshot, available.