I've got a newer Audi A6 and while it sounds decent, it is nothing close to my Toyota Sequoia SUV custom system (Alpine, Audison amp, Hertz speakers in pods, sound deadending second skin products, etc.). I've also rode in a few new higher end BMWs with "upgraded" systems that are a big step forward, but you're in the $75K to $100K range and out of my budget.
I had looked at doing upgrades to the A6 and found out the factory head systems just feed elaborate dsp & eq devices made to make mediocre / bose speakers put in poor locations sound decent. The oem speakers I've seen in even these higher end German cars are cheap generic speakers. The factory head systems are also often burdened with navigation, bells and whistles, displays, dvds,etc. The factory speaker locations are also typically choose for appearances and not sound quality. Only recently have I seen them start putting at least the tweeters up in the A-pillars. It's typically no longer possible to just drop in upgraded / audiophile speaker drivers because the factory DSP / EQ can't be tweeked back to a near flat / normal response and make them sound right.
It has become a real hair ball to retrofit a higher end amp and speaker systems in most of the newer cars. In order to continue to use their OEM head unit displays, you end up needing to reverse engineer EQ'ing their settings in order to get real audiophile speakers to sound right (insert new DSP unit). You will also end up needing to bypass the factory amp because it can be part of the DSP box and electronics (insert new Amp). It can all be done, and sound much better, but figure on a minimum of $3K to $5K+ I finally gave up and said the A6 is good enough - it's the wifes daily driver and now when we go on long road trips I'll just use my Etymotics and JDS labs Altoids mint can amp for sonic bliss.
To see some real s.o.t.a. automobile audiophile sound systems, check out the recent TONEAudio issues. The most recent is an ultra cool Porsche 911 Carrera with a Burmester sound system. Check it out at tonepublications dot com There are some other back issues with Jeff test driving similar awesome cars and sound systems as well. If these are in your budget range, then, yes, there are some automobiles with (as close as possible) audiophile sound systems.
Kenreau