My first post. yay.

Excuse me if I ramble for a moment...
I'm fortunate to have a top-notch pro in town that takes care of this for me. In my 2010 328i I had them add a 600 watt 6 channel amp, a sub and replace the speakers with Hertz speakers. The car was only a couple months old so I told them I wanted it to appear as if it came from the factory. They did a fantastic job, you would never know it had been done other than the sound. My BMW dealer actually recomends them as well but I already knew about them anyway. They have been around almost 30 years.
I now have a F30 335i sport line with the HK (ya again). I can say that for a factory installed system, the HK is quite impressive. 16-18 speakers + a 9 channel 650 amp in the trunk by the fusebox; subs under each front seat, full surround sound with surround DVDs and the L7 mode that performs pseudo surround that claims each person in the car experiences similar stereo imaging IIRC

I'll still likely upgrade the amp and speakers in this car though simply because I spent so many years in the audio/music world, its one of my hobbies; that also allows me to know if the guy I hire knows what he is talking about.
If the non-HK system has an external amp there is the advantage of the radio having a dedicated line out. In my 2010 328 with the base 4-speaker system, there was no line out. We had to use a pricey converter to properly reduce an already amplified signal back down to a useable clean line level.
The disadvantage of upgrading an external amp (at least with the 2012 HK and maybe the stock?) is that some of its functions are likely controlled by the radio unit such as the L7 setting) etc. The amp is somewhat custom purposed so there is the slight chance of not finding an aftermarket amp to meet all the specs without losing functionality or a chance that there is a proprietary link between iDrive and the amp. Not sure if I can find a 1200 watt 9 channel amp either. I think its possible to swap out the amp but someone is going to have to be good enough to figure out what functions are what and mate that to the new amp. So yes, could be complicated but possible in the right hands. Let me iterate that I feel quite lucky to have someone who can do this work this well, they are like the west coast customs of car audio in my town. If it can be done, they will know.
A few things I have learned about the HK:
As noted above the L7 surround setting sounds incredible with a great DVD that is surround sound encoded. It also modifies 2 channel stereo signals to provide a similar experience regardless of seating position and it also makes voice/vocals more intelligible. I'm pretty sure some of this is achieved by running a summed mono version to the center speaker and some other tricks.
If you spend most of your time listening to regular ole stereo (CDs, MP3s, Satellite Radio) you might occassionaly turn the L7 surround on or off depending on the material. L7 adds quite a bit of lower midrange and pushes center content hard center. Some stereo content sounds great with L7 on other songs sound much better with it off. I switch between the two often (I have button 7 set to Tone Settings). I noticed there are threads with some EQ curves that vastly improve the sound of the system. Be aware of which mode you are using when adjusting EQ, if you are reducing low mids that are there due to L7 being on, you'd likely be better to just turn L7 off.
The system is good enough to expose bad mixing and mastering. This means one CD or MP3 may sound unbelievably good and another horrible in comparison. I have about 1000 high quality MP3s on USB and CDs with music from the 70s thru the present and their sonic quality varies wildly. This isn't the system, it isn't the medium its bad recording and production. Satellite is hit and miss by the way, if you want to experience how good the HK sounds use a CD or high quality MP3. Satellite, just doesn't do it justice.
The subs under the seats appear to be bolted to the frame, there is a metal grill in the carpet so they are flush under the floor. I assume there is some protection for a spilled liquid because it sorta looks like a drain.
Minor annoyance... The entire media portion of iDrive follows the volume button for the most part. For example if you insert a DVD and the volume is all the way down it is effectively paused. The screen will go blank as if it were going to play but you'll sit there for 5 minutes waiting and thinking its broken. Just remember to turn the volume up and it should play as normal.
Lastly, I think the HK's bass response is at its best around 95-125 hz. Its real punchy in a good way but would be nice if it extended (or rolled off less) in the 60-80 hz range. I've heard it reproduce in that range, but I think it could use just a few dB more there. Highs could be a tad better above 8k but I'm splitting hairs here because overall you can tell it is a well tuned system, its not hyped but well tuned if that makes sense.
It will be another month or so before I see "my guy" on the difficulty of an upgrade, I'll post back with the verdict. No, I'm not normally this long-winded, its basically one big HK brain dump.