The overlay deliberately suspends pointer restrictions when it's open to allow users to get out of game windows and into other things, so that is expected. The fact that you can scroll the desktop then is an unintended side effect but also expected if games fullscreen in certain ways. I'm not sure we can easily change this but we'll take a look.
After discussion, this is basically expected given the way games and the system do fullscreening. Steam wants to break grabs, so that isn't going to change either, and the end result doesn't appear to be causing any problems so I don't think anything's going to change in this area.
With some games, in an old specs system (like me) when i am in a Team Fortress 2 or Killing Floor in a game, and i open the Steam overlay and move out the mouse of the screen, although you don't click the screen changes to desktop resolution and with the game running it's very annoying because i have to wait some time until i can click inside the window and restore the game. It isn't a fatal error because even with my old specs only i have to wait and all is working well, but you can't expect all the games will run correctly if you shack the system like that with the game working.
Other problem is the window manager effects aren't disabled with this configuration. KWin (in my case) or other like compiz, suspend the 3D effects with a fullscreen application automaticly, but with that behaviour it doesn't do anything and the FPS in all games is much lower. I have to suspend the effects manually.
I understand you closed this issue, this isn't a high priority issue, it haven't any hard problem with games, but it is a strange behaviour that it could cause some problems in the future. If you can lock the mouse for it doesn't move out of the display, but it's more important the impact of the games of this behaviour and the problem of the 3D window manager effects that Steam don't switched off correctly, maybe Steam can do this with some detection and options in configuration.
Sorry for the long text, it's only my opinion.
The reason we closed the issue is that we don't have a practical way of determining whether the system is going to do something bad or not. You mention that your system and window manager have some downsides but others don't. Trying to check all possibilities and identify when it's a good idea to break grabs and when it isn't is not something we can reasonably do. We can keep this open to try and add some simple approximations, but it's unlikely anything will change in the short tem.
I tested this with Killing Floor and Superbrothers: Sword & Sworcery
I have a 1280x800 desktop resolution. These games when i change the resolution to lower (for example, 800x600) all the game is working well, but if i hit alt+tab to open Steam Overlay and move the mouse pointer beyond bottom-right, i can view the Steam client behind like this:
I can move with the pointer across all the desktop (it's in my desktop resolution, but my vision is lower), and if i click out of the game window it's come to my desktop resolution. If i click again in the window game it go to the game resolution again.
~~Other games i tested don't go to other resolution directly. You can view the issue here https://github.com/ValveSoftware/steam-for-linux/issues/676~~ Not related.
My specs: KUbuntu 12.04.1, KDE 4.8.5