You wondered correctly.
Installed 10.9 on a partition on the internal HDD. Then proceeded to reformat each of another internal HDD partition; a USB external partition; and a flash drive.
'Ignore ownership' defaults were:
internal UNCHECKED
external CHECKED
flash CHECKED
The above is 'correct', yes? It makes sense for removables to default to permissionlessness.
This is exactly the behavior I see on 10.9.2 and from what I read around different sites, should be the default.
Then used Migration Assistant to bring over 'computer settings' only. I believe this was <200KB in size. From the values in volinfo.database I could see that this was one of the migrated files, but I think that's besides the point. Reformatted the three volumes again, and:
internal UNCHECKED
external UNCHECKED
flash CHECKED
So there you have it. Something that's migrated in 'computer settings' is changing the default 'ignore ownership' setting for a newly erased USB HDD drive.
So like you suspected, volinfo.database does come over as part of Migration Assistant. If you delete volinfo.database after this migration do all externals default back to checked? Odd.