How can I find out what the App Store is automatically downloading? I can see via Activity Monitor that storedownloadd is receiving a lot of packets and responsible for my ~1mb download. When opening the App Store, I can see only one update (Xcode 8). Can I deduce that this is what's being downloaded?

If not, how can I?
The App Store may not record exactly what everything it does is, but you can try looking a couple places:

/Library/Receipts/InstallHistory.plist has a list of program installation history for the computer (most recent installation at the bottom, with the highest numbered entry). 

/Library/Preferences/com.apple.SoftwareUpdate.plist will give you the number of pending updates as well as the last time the App Store checked for updates.

You could also try running /usr/sbin/softwareupdate --dump-state, which dumps the current state of the update daemon to /var/log/install.log.

(As a side note, in my experience XCode updates are usually over 1 GB in size, so an XCode update would definitely run for an extended period and download lots of data.)