I have no idea why sleeping too long seems to have a negative effect. I'm guessing that whatever chemicals your body is producing might add up and you have too much when you wake up.
And because setting the alarm to the same time each day isn't going to work when I stay up late fall right back asleep after the alarm wakes me, I tend to set it roughly 9 hours and 30 minutes after I go to bed, and the Sleep Cycle Alarm app handles the rest.
On falling right back asleep, one thing that has proven awesome is taking my Adderall regardless of whether I feel like getting up. Then, if I fall back asleep, I wake up not too long later feeling extremely refreshed and ready to tackle the day.
It's so good, in fact, that I think it might be beneficial to set the alarm 30 minutes earlier to fall asleep on Adderall. Of course, using the "Sleep Cycle Napping" app to make sure I wake up 30 minutes later, because sometimes I just sleep another 2 hours. I'm guessing you could do something like this with any morning bedside stimulant and get similar benefits.