what is this= missing bundle path; skipping (when running software update --download -all, files and processes)

no, not concerned, just wanted to make sure it was not messing with sofwareupdate -d -a

why does it say 'packages have been saved to /Library/Updates'?
what packages is it talking about, i don't see any downloaded updates.

They're there, but in sub folders within /Library/Updates/ Poke around and you'll see them, or should, it anything actually got downloaded.

so when the software update -d -a runs and finds available updates it downloads them into /Library/Updates ?

JSS would then be able to tell via smart group (criteria: number of available updates IS NOT 0) and let me know which computers have updates to install ?

I'm not certain about that. I'm not sure if the jamf binary checks for updates downloaded into /Library/Updates/ as I've never actually tested that. I believe it only gathers the updates and number of updates available during an inventory collection, so in essence like running sudo softwareupdate -l and parsing the output to see what updates a system needs and a total count.
Someone please correct me if I'm wrong. Its been a while since I used that feature so I'm not clear on that at the moment.

You could on the other hand, create an Extension Attribute to capture the packages located in /Library/Updates/, and another one that also gives you a count in a standard integer format.

I just had a computer get the following result, but it doesn't say anything like Done.
Packages have been saved to /Library/Updates

are these firmware updates considered different than OS X software updates?

Executing Policy TEST 2 Software Updates using files and processes...
Running command softwareupdate --download --all...
Result of command:
Software Update Tool
Copyright 2002-2012 Apple Inc.

Finding available software

Downloaded Thunderbolt Display Firmware Update
Done.
Running Recon...
Retrieving inventory preferences from https://casper.blobface.xxx:8443/...
Locating package receipts...
Locating accounts...
Searching path: /Applications
Locating plugins...
Locating printers...
Gathering application usage information...

Firmware updates are considered software updates. Software updates are more than just updates to the core OS version or to installed applications. It should have downloaded it to /Library/Updates/ just like anything else.
In fact, in a recent test I had done on a Mac, it had a pending firmware update available and softwareupdate -da downloaded it into /Library/Updates/ just like all the others.

now i'm waiting for my Smart Group to populate with this information that a mac has more than 0 available updates

I just received another softwareupdate --download --all result, it looks like it was downloading the updates and then never got to the line 'Packages have been saved to /Library/Updates'

Executing Policy TEST 2 Software Updates using files and processes...
Running command softwareupdate --download --all...
Result of command:
Software Update Tool
Copyright 2002-2012 Apple Inc.

Finding available software

Downloaded iTunes
Downloaded Safari
Downloaded Security Update 2015-001
Downloaded Remote Desktop Client Update
Downloaded iBooks Update
Done.
Mar 2 14:03:17 wkstn225-197.ddd.blobface.xxx softwareupdate CLI[18740] : /usr/sbin/softwareupdate: XPC error in __60-[SUCommandLineTool _runSessionWithUpdates:skippingInstall:]_block_invoke (Error Domain=NSCocoaErrorDomain Code=4099 "Couldn’t communicate with a helper application." (The connection was invalidated from this process.) UserInfo=0x7fa8d8505150 {NSDebugDescription=The connection was invalidated from this process.})
Running Recon...
Retrieving inventory preferences from https://casper.blobface.xxx:8443/...
Locating accounts...
Searching path: /Applications
Locating package receipts...
Locating plugins...
Locating printers...
Gathering application usage information...