If Steam is being run as administrator, and MO is not being run as administrator, MO is unable to detect Steam or affect the App ID of an executable started through MO.
The most noticeable effect of this is that MO will constantly tell the user that Steam is not running. This isn't an issue by itself as it's correctly telling the user that there's a problem. The message could be updated to mention the possibility of Steam being run as admin causing a problem. If the message is changed, the "remember choice" flags should be cleared so users get the new message when updating.
Next, trying to run a script extender (SKSE, F4SE, Enderal SKSE) will likely cause the original launcher of the executable to run. This is due to the SteamStub DRM. The script extenders bypass this behavior by providing an App ID for the executable, making SteamStub think the executable was launched normally.
Finally, due to the SteamStub behavior mentioned above, the wrong game installation may be launched. This can occur in innocuous cases like Enderal launching Skyrim or in more odd cases like Skyrim launching a different Skyrim installation. That one may occur if the user has messed up moving the game install. At best, the game launches normally but has no mods as USVFS doesn't know the correct location. At worst, the wrong game launches entirely.
If Steam is being run as administrator, and MO is not being run as administrator, MO is unable to detect Steam or affect the App ID of an executable started through MO.
The most noticeable effect of this is that MO will constantly tell the user that Steam is not running. This isn't an issue by itself as it's correctly telling the user that there's a problem. The message could be updated to mention the possibility of Steam being run as admin causing a problem. If the message is changed, the "remember choice" flags should be cleared so users get the new message when updating.
Next, trying to run a script extender (SKSE, F4SE, Enderal SKSE) will likely cause the original launcher of the executable to run. This is due to the SteamStub DRM. The script extenders bypass this behavior by providing an App ID for the executable, making SteamStub think the executable was launched normally.
Finally, due to the SteamStub behavior mentioned above, the wrong game installation may be launched. This can occur in innocuous cases like Enderal launching Skyrim or in more odd cases like Skyrim launching a different Skyrim installation. That one may occur if the user has messed up moving the game install. At best, the game launches normally but has no mods as USVFS doesn't know the correct location. At worst, the wrong game launches entirely.