if Shrek is a semi-midget ogre...

Well the potion was supposed to make you hot. He was also pot-belly as an ogre. Nothing about Ogre Shrek was hot. The potion changed all that. Fit and tall is what's considered standard hot, not short and fat.

The bottle says "You both will be fine, happiness comfort and beauty divine."

But then another thing to consider, Shrek is just small for an Ogre. But even as a runt ogre, he's still bigger than the average human possibly. So when he became human, he's still tall. Lets say orge Shrek is 6'4. That's tall for a human. But if the average height for an ogre is 7'0, then yeah, he's still a runt, because he's below average for his species.