Hi and welcome to Arturia forums.
On the original hardware Yamaha CS-80 the presets was only consisting of the settings in the two synth lines.
I believe the stored synth lines parameters could not be used for stored settings/ presets.
The stored settings in Yamahas original hardware CS-80 was settings for resistors, and as we are talking about a late 1970's synth, then i don't think you in any synth found a pick-up function on any parameter.
So Arturias version actually only set the same parameters for the "Hardware presets", that the original did, when you select a preset using the GUIs preset buttons, and as such your observations about this is correct.
Arturias version have the extra features that the stored parameter settings change, and that you can edit all parameters for the stored presets. And if you use Arturias preset browser system, them all parameters are stored and recalled. And you have a lot more presets than the original Yamaha have then.
The original hardware Yamaha CS-80 only had 2 user presets for each synth line. They where settings set in a panel under the hood. (Miniature synth line parameters.)
Unfortunately in Arturias version i don't think the original hardware presets sound correct.
And the preset buttons themselfs should not light up, when you select a preset in Arturis own preset system, as they do not use the sounds stored in those buttons. That's why you can select an allready select preset button and get a change in sound.
The two user buttons could either work for user settings, or light up when a preset is selected in Arturias preset system. It's not ideal as it is, and it can also be confusing, like it look like you are confused about this.
Some of Arturias CS-80 parameters does'nt work excactly like the originals did.
I believe it's possible to find manuals for the original Yamaha CS-80 on the web. You can also find pictures, videos, and articles about it.