Rake and trail both change when altering ride height, lowering forks in triples or raising/lowering the rear. All of which factor in to handling.
Has anyone actaully measured the wheelbase of a lowered bike compared to stock ride height? For a slammed bike, you might be surprise to find it is a bit longer than stock (1395mm vs 1422mm for mine). While you are lowering the front only, it steepens the angle, but when you lower the rear, it has the opposite effect and brings it back to the same angle. The swingarm is already down from the pivot, but when lowered, it is level with the pivot which lengthens it (ever wonder why your chain gets TIGHTER when you compress the suspension?).
Pulling up the forks to lower the front, decrease the rake (steeper angle) and shortens the trail due to the increased angle of the rake. WHile this does sharpen up steering, depending on suspension, tires and such...it can have a negative effect on stability. Raising the rear ride height also does the same thing. This can help you understand some of the terms and such...
http://www.carbibles.com/suspension_bible_bikes.html
What one perceives as bad handling to one person, another may not even notice.
I'd still like to know just how lowering a bike will cause the forks to bottom out.