They do it so you remember Lincoln not the model, makes perfect sense actually. Except they could be slightly less confusing by using a first letter to designate SUV vs car like Audi A for cars Q for SUV
It doesn't make sense to use random letters though.
Look at Mazda... 2, 3, 5, 6, CX-7, CX-9. The bigger the number, the bigger the vehicle. Makes sense.
Audi, BMW, all make sense. Like you said, A is for their cars, S for their performance, RS for ultra-performance, followed by numbers to indicate the class of the car. Similar with BMW.
Acura is getting as complicated as Lincoln too... if you have no previous knowledge of Acura's lineup, would you know what CSX, TSX, TL, RL, MDX, RDX, ZDX and whatever else is? Either you go will distinct and recognizable names (Accord, Civic, Corolla, etc.) that customers can learn and remember over the years, or you go with a number/letter approach that makes sense!