I have read on the forum that we should pay some percentage over dealer invoice for an A4 (such as 5% to 7%). I have also read here that we should pay a particular dollar amount over invoice (such as $1500 to $1700). Due to the price difference between the 1.8T and the 2.8, the percentage calculation results in different dollar amounts. My question is: should the dealer make a greater amount of money on a car that costs more, or should the dealer make some particular dollar amount regardless of the cost of the car? Thanks in advance for your responses.

There is no exact or absolute. Circumstances will account for 2%/$500 variance, at a minimum. For example, you can get a better (lower markup) deal right now on a 2.8 Tip. (~33-36k) than you can on a 1.8T 5spd. (~26-29k) because of production-driven availability situation. Or, end-of-month/lots of your favorite color in stock/cancelled order weird option combo. sitting there/etc. will affect spot pricing practices.