Hi Robert,
Your getting closer!
First, yes dtoverlay config files are for HAT cards and only the file for the installed HAT will load at boot. Don't worry as long as the product description the for HAT you want says it has an EEProm. Additionally dtparam entries modify other boot settings and load addtional drivers only if they are needed.
https://www.raspberrypi.org/documentation/configuration/device-tree.md Second, yes again the IdPi Firmware sold by JRiver is may not be the latest used by Raspian Stretch with Desktop. Only the HATS in the IdPi firmware will work. Raspberry Pi Org keeps the drivers in it's own distribution up to date.
Third, the sudo apt-get command is used to periodically update the whole running system of any Linux distribution. Unlike Windows or Mac you have to update Linux manually. So yes, if there has been a new HAT released then it will be available in the current build of the kernel used by Raspian OS, just update and go.
The main benefit, for me, of server programs like JRiver IdPi is that it will reboot if the program crashes or the power goes on and off. The Raspian Linux version does not reboot without installing a lot of other code to detect if JRiver is running or not. If, like me, you are not a Linux guru the IdPi is easier.
I checked the Overlay directory just now and these are the cards which are listed and readily available:
iqaudio Dac/Dac+/digi
justboom dac/digi
allo piano dac
Pi2 Design 502dac
I think all of these auto configure.
Do you currently have a Raspberry Pi 3 to play around with?
I am enjoying the conversation so I am ready to answer any other questions I feel confident about. JRiver always remains our reference standard.
Duncan