Say that I get a pinyin promt that I find way to easy and I want to mark it as a four. I can't press four like with the other promts because four is still the keybord shortcut to change to the fourth tone.

Is there any way around this? Or is reaching for the mouse to tick the little green button the only way?

That's currently the only way. It's pretty high on my list to get the grading buttons into the reading prompts, too, though. That'll not only allow easier 1-4 grading, but also make it easier to do the reading prompts without typing. Not quite sure when I'll get it, but I'm itching to have it myself.