A toggle for "Always on Top" is an easy addition. I'll add it in!
As for the second suggestion... it should do this already? (I'm earning points right now as I type this) I disabled the mouse when the game isn't selected because it messed with my mouse sensitivity when playing other games, but keyboard and Xbox controller inputs should earn points when the game is in the background. It is supposed to be a background idle game that you come back to every so often to open a pack of cards. If keyboard inputs aren't working for you, I can try to investigate what is going wrong there. (Because clicking 2000 times in a small window is in fact not very fun at all!)