Yea, the multi-tasking UI is especially half baked. You should be able to have two instances of the same app side-by-side (at least Safari).
There's no reason this needs to be an OS feature, and at least one good reason why it shouldn't be: data integrity. Threading is hard enough for most programmers to get right, and now you want to require IPC and/or coordinated access to every apps' data files?
I love that this is already being provided by an enterprising app developer, but I hope they get Sherlocked.