Alright, I get the confusion now, sorry about that (and then I was on vacation, go fig).
First off, I didn't mean we have something in the works, just that we had identified that this would be something that would probably be desired and did not, at the time, have a better solution in place. I will see if it's possible for us to do unattended LM registration through Setup in the future, but it's not an active item at present. I agree that it seems like a lack in the current system, and I'll see if we can get that functionality in some way in the future. It would be as completely new functionality though, not as a bugfix.
To the specific case, good idea with ARPSYSTEMCOMPONENT. I see why that doesn't work, but it made me think of a different idea. It's a couple steps (and I probably wouldn't suggest it if it wasn't clear that I'm pretty sure you know what you are doing here) , but it should actually resolve the add/remove programs issue. The reason the ARP information doesn't show up is that it's actually installed by a different component, through Setup, for various reasons. So what you could do is install both Setup+ARP first, and then Scan Connect through the msi. Here's the steps you'd take:
1) Make a copy of your Scan Connect installation and remove the two ScanConnect msi files from the Setup directory. This will cause Setup to just skip the main SC installation package.
2) Run a silent install on that Setup package. Since the main SC package isn't present, it won't give you hardware instance issues. This will setup the Add/Remove programs element as well as some other niceties.
3) Install the Scan Connect msi directly through msiexec along with your license file.
I tried this one out, and in the end it should basically get you what you are looking for. You'll be able to bulk install Scan Connect without having to individually register each instance in the LM separately, while still having a complete installation.
To the licensing question itself, yes, the license agreement stipulates that you must be licensed for the amount of machines that you install Scan Connect on. License manager registration is not strictly speaking mandatory for that.