I think that Rob and Cristian have really answered most of your questions except for one thing. Even though you mention that you are a hobbiest and not making products for commercial selling you do seem concerened about how programs get initially loaded
into a Cygnal controller in a non-development environment. There are two possibilities here. One which I use and the other is an option for you to consider.

First off Cygnal offers a Windows DLL that provides a full interface between a target processor and a windows program via a PC serial port and the Cygnal EC-2 adapter. One can write customized production programming software that uses this DLL to program the FLASH from a HEX file. I am in the process of doing this with a Visual Basic program.

Second, if you come up with a wizbang idea for a product that can sell 1000's or 1000000's then you can contact a distributer that sells the Cygnal parts and also offers a programming service. They will program the bare parts for you to a program pattern that you specify. Typically there is an up-charge for this service. One client I work with uses Motorola 'GP32 parts in their product line and has the vendor program them for about $0.50 per part. It turns out much cheaper for them than committing a programming step in their production flow.

With any ISP solution it is of course necessary to provide access to the ISP signals in the target product. In the case of Cygnal this would be the JTAG port plus the target VDD / GND connections. It is not necessary to burden the target product with the same 2x5 0.1 inch style connector that the EC-2 uses however. Here is a picture of one method where the target used a small 10 pin flex strip connector. An adapter was built to adapt the flex strip to the EC-2 connector.
The Cable Source
The Connector Photo

In another product we put down a 2 mm surface mount header from Moles and I built an adapter to the Cygnal EC-2 cable.
The 2mm Header
My 2mm Adapter.

Michael Karas