I just recently tested the re-sync capability of the latest version of Insync. Turns out it’s got much better than when I wrote that post. During initial setup, it can now automatically and correctly decide which folders should be synced, and which ones should not, and there doesn’t seem to be any duplicate issues.
The post I wrote is still relevant for resync that’s not during initial setup. But at least for initial setup, using Insync in a straightforward way appears to be good enough now.