This is what I think will be the last update.
The BOSE sub woofer doesn't fit directly because it has a plug with five wires and the std sub only has two.
What have I learned so far?
Std sound system have:
Two tweeters on top of each side of the dash.
Front and rear doors has a 6,5" woofer.
Rear doors have a tweeter.
In the parcel shelf is a sub woofer, think its 10" but could be 12".
All driven by std no-name amplifier.
BOSE sound system has all above but:
One more tweeter in the middle of the dash (next to the wind shield as the others)
Two woofers in each side of the parcel shelf.
And there is a 12" sub woofer in the middle of the parcel shelf.
The tweeter in the rear doors are the same for std and BOSE sound system, all other are different.
All driven by BOSE amplifier.
If you are planning to "upgrade" from std to BOSE, you can only replace the speakers that are mounted in the std setup, there are simply no wires or channels from the amp for more speakers.
Going from std or even BOSE to B&O, I think it will be bigger headache than I will recommend.
So for those with itchy fingers that like to think outside the box, while using mostly the same locations for the speakers. Is there any possibilities? Of course there is, but you would need some tools and fabrication skills. This should apply to both std and BOSE sound system. To start off in the front of the car, you should decided if you go for two or three tweeter if have BOSE, std have only two so there its easy. I would abandon the holes under the cover and mount them on top with a screw or double sided tape. The holes has limited depth, at least the left (or was it the right?), so to make it easy I would recommend top mounting. Maybe some with an angle housing or just flat to bounce off of the wind shield. The doors has the same 6,5", but the back cover is slightly different, but shouldn't make any difference in choosing speaker. The only thing to think about is that the total depth should be less than 63mm. Passive cross-over may be a challenge for the front door woofer/dash tweeter as I think it would be a deep dig to find where the cables split to the woofer in the door and tweeter on the dash. I see some two-way sets has only cross-over for the tweeter and just full range for the woofer, while other has a dedicated two-way crossover box. There is also a possibility to take apart the two-way crossover and reassemble it in two pieces, one for the woofer and the other for the tweeter.
For the rear doors it would be easy as the woofer and tweeter are mounted not far from each other. For the tweeter in the rear doors, I didn't have a closer look at as it was the same in std and BOSE, but anyway I would go for the same as in the front to get the same sound. Mounting of the tweeter could be possible under the cover, if not, just mount them on the surface of the door panel.
In the parcel shelf std has non woofers so that makes it easy, and BOSE has two, but I don't know the size of them although I won't be surprised if they are 6,5" too.
For the sub woofer, the std sub will be easy to replace with any other sub as it has two wires inn, some fabrication for a bracket would most likely be needed. The BOSE sub would be a little bit more tricky to replace as it has five wires going into it, but I've read online some has made a splitter to take out the signal and feed it into a normal car amp and then to the sub. Another thing with replacing the sub is that both the std and BOSE is very low profile, so you may need to cut out some to get room for the magnet and/or speaker housing.
The big frustration with modern cars is that the sound system is so integrated into the car and the amplifier has proprietary connection that doesn't follow any standard.
So, in the end. If I knew what I know now before I started, would I have done it differently? Good question, but probably not. Although tempting to go for even better speakers, I think (without knowing) that the std amp would quickly be the thing that holds it back. Expecting that the BOSE amp is better, it would actually be more tempting to do some serious upgrades if I had a BOSE sound system as a starting point.
Thanks for reading!