In the course of working on the improved offline experience for Orcas, we discovered that going online with Get Latest On Checkout turned on was rather painful. Specifically, you would never get a chance to generate a version conflict. This, in turn, meant you would not be offered an opportunity to merge your "offline" local changes with the server if there was a newer version on the server when you went online. This is due to the fact that you pended the edit against the tip version of the file, so all conflict generation regards you as being at tip.
To get around this difficulty, we decided to update our API and add a new flag to the PendChangesOptions parameter in Workspace.PendEdit. This flag is, ForceCheckOutLocalVersion, and it will cause "GetLatestOnCheckout" to be bypassed for this PendEdit call. The PendEdit call is forced to pend an edit against the version of the file that is present locally in your workspace regardless of whether the client or team project "GetLatestOnCheckout" setting is active.
The ForceCheckOutLocalVersion flag did not make it into the Orcas Beta1 release, but it should be available in a later release.