Yeah, it's only a third like the $ earnings.
I think I will change this.
As you mentioned the current system forces the player to keep the window open.
I think I'll do:
100% earning and research while not in the minigame. One can collect research AND money after coming back.
The research (hour glass) will be something different. Don't know what yet.
Your idea with "100% earning and research while not in the minigame" from start actually sounds pretty good. Considering the many hours it takes to reach the (hour glass) research, my previous post suggesting 50% and then research to get 100% would still push players to leave the minigame open to half the number of hours for research, so it would not solve the problem. The minigame is part of all 3 paths, so players doing all the paths actually have to play through it 3 times until they have earned a significant amount of Prestige.
Having the research (hour glass) give a bonus while not in the minigame would still be useful to let players play the rest of the game including the other minigames, so maybe even give a small bonus depending on "played" days or ingame interactions.
Main problem with letting the minigame run on its own is that some of the achievements require a lot of player activity to restart the minigame and upgrade stores again and again to get powerful boni like +% Prestige and -% upgrade costs. I noticed that at higher level the player may restart every 1-2 min and the specific achievement requires hundreds of restarts to complete, so the player can be easily caught in an endless loop restart - upgrade - restart - upgrade - .... So maybe even consider to connect restart conditions with playing the rest of the game and passing days, eg restart only once per ingame day. After all playing the minigame is just activity inside one timeslot and doesn't even cost AP, it can even be completed/maxed out in the timeslot it is unlocked.
On the other side be careful with changes to not accidentially remove the fun from the minigame ... (or preserve the current version of the minigame as a separate minigame which can be accessed from main menu and maybe played against the clock with highscore etc.)