The downside, of course, is that setting this to true would only work out if the authors did structure each localisation 100% identically.

Yep, that's exactly my concern, it really would have to be 100% identical - if someone was to change that option otherwise it would cause a lot of problems.

Also I'm assuming that the Localisation feature will eventually be implemented in the Authoring Tool where I don't think it would be possible to create two structurally identical courses... although saying that it is possible to ensure config options are not displayed within the authoring tool - you just leave them out of the properties.schema.

I'm pretty sure that Ryan Olds said he was going to amend one of his localised courses so that it wouldn't reset on language change (because he knew for sure the languages were identical); so if that is something you need he might well share what changes he made if you ask.