Is there anyway to get a list of non-default gateway settings? Currently these are stored in the local DB, correct? If so, I assume we could query for settings?
You could use SQLite's sqldiff tool to compare an extant config.idb against a brand-new one from a test system. You'll have to have the same modules installed and be on the same version to have a fair "baseline" for the comparison.
It might be possible to recursively extract actual table data that differs from default values entirely within the one SQLite DB, but I wouldn't really approach the problem that way.
I would also ask why you need this 
Need might be a strong word, more of a nice to have. Basically, I would like to know from a quick glance what settings have changed. I have had a few occasions where some turd changed something and didn't know it (not sure how). Or, perhaps a way to get a list of settings to forward to someone else so they can setup a gateway similarly.
sqldiff would output an executable string of SQL statements you can run to make one gateway's config exactly match the other. Probably as good as you can hope for in this case; if you run those statements (with the gateway offline) and then start it up it has no way to distinguish the two.