It depends on how they have the crossover set up. It is definitely possible for the crossover to affect things other than just at the crossover point. There are "EQ" circuits that can be used to reduce inherent "peaks" in a drivers response. Also, there will almost always be some form of attenuation circuit on the tweeter. For some reason tweeters naturally have higher effeciency, so they need to be "quieted down". This is usually just a resistor or two. If Boston was going to make an adjustable crossover, it would have been wise for them to make it possible to adjust the relative level of the tweeter, which in your case might have taken care of the "shrill" sound you were hearing. I've noticed this about their home speakers as well. One pair that was particularly expensive, and had an aluminum tweeter, about made my ears bleed. The silibance was soo horrible, I had to switch to listening to different speakers. Maybe all of their speaker designers are 70-year-old construction workers that don't have hearing left above 5kHz?

On a side note, the receiver in the car should have enough EQ ability to tame down most of the high end harshness. Once the car is moving, there is a lot of road noise, which dramatically affects your perception of sound. Maybe the speakers are optimized for that type of environment, and would thus sound very different when installed in a car? Seems to me like $1000 is an aweful lot to spend on car speakers...

Jason