As long as you don't press "Power Off" too soon after the first "Stop", that wouldn't be a problem.
But if "Stop" then "Stop"+"Power Off" is often pressed in quick succession, then adding another command between is a good idea, and "Back" would be a good one as it is non-destructive; i.e. Goes back up one menu level, or doesn't nothing if already on the top menu.
You could also add a pause\wait time at the beginning of the "Stop"+"Power Off" sequence, I think, on many remotes. I haven't actually checked if that is possible on a Harmony remote.
I suspect a one second pause\wait would prevent the double Stop from clearing any Bookmark. Some testing should sort that out. The remote would have to be pointing at your HTPC for the full pause\wait time though I suspect, so that commands are received, as I think any pause\wait on a Harmony is executed in the remote, and then the following commands would be sent.