There's no underlying "basic compare command", it's just the way people want synching to work in almost all cases, and the only way synching can work in the general case (where two files may have the same names in different directories and thus cannot be resolved to a single flat destination).
What would adding a TeraCopy copy-and-verify to an intermediate folder get you, other than more complexity? You'd just be duplicating your source folders and then synching the duplicate to your destination, which doesn't seem to get you anywhere. Synching the copies is the same job as synching the originals, and that's the part that's problematic.
With this and your other thread (which are both really the same question, I think?), it seems like you are layering on more and more tools and complexity in an attempt to work around a fairly ridiculous limitation of the "database" tool you are using. It would make a lot more sense to replace that one tool with one that understands folders than to build a Rube Goldberg machine to auto-sync folders into a flat list.