But sometimes I want to actually open the overlay >_>
It happens only first time you use shift after alt-tabbing or showing overlay, the easy way to cope with this issue without blocking overlay is to hit and hold shift button at the very beginning of the game, just after issuing first orders. The overlay will show up and hide itself, then you can unhold your shift and use it normally till the end of the match, it never shows up twice. (As long as you don't use overlay during game but who does that?). Just remember not to issue shift orders during that first "overlay shift" as game doesn't record it's pressed then.