If the '07 has the "smart" alternator setup you will be unable to bypass it alarming without reprogramming the BCM. It looks for certain reactions to its adjustments and if it doesn't see them it will trip a code. Also, why are you trying to max out the voltage? If it bothers you THAT bad, add another alternator and battery. Run the second battery at max voltage and be done with it. I did this. All it costs is a bracket since you already have a second alternator, maybe a bracket and a second battery(I say maybe a second bracket because I believe you already have the bracket for the second battery from the factory). Would suggest staying away from Optima batteries and just get a good quality AGM. There are some characteristics of the Optima batteries that make them undesirable in a daily driven car or truck.
If you have a modern, high quality amplifier they don't care what the incoming voltage is. Only older or cheap amplifiers care what the incoming voltage is anymore. Modern amplifiers are designed with the smart alternators in mind and won't benefit from the higher voltages you are proposing. Running your voltage high will only cost you gas mileage and not benefit you at all. Modern Amplifiers use Pre amplifier capacitors to store energy for the high requirements of a sudden high output such as a heavy bass beat. These basically make a large Capacitor obsolete because they accomplish the same function. These also regulate the voltage down to match the capacitors so a higher voltage will do nothing for you. I would assume if you have a 6000 watt system that you are using good quality, modern amplifiers. If you are using cheap amplifiers, no way you are running 6000 watts.
If we consider: Volts * Amperage = Watts and to consider how many amps we need we switch this around to amperage = watts / volts. So we plug in your numbers at 12 volts: Amperage = 6000 / 12 = 500 amp. This will need a very large wire.
Same using 14 volts as an easier to use number would still be 6000 / 14 = 429 amps which still needs a huge wire.
What size is you alternator again? To output at 6000 watts you would need AT LEAST a 550 amp alternator if we assume you had a 120 amp alternator from the factory. This assumes a constant 6000 watt usage.
Please note that this does NOT take into account voltage drop in the wire which is about 5% per foot in a standard automotive wire. This number is not static however. The more amperage you put through the wire the more voltage drop you will get once you get past the thresh hold of the wire. So distance is a factor as well.
Lets assume you are using a high quality wire which is only a 2% drop and you are running 15 foot of wire to get from the battery to the back of the truck where you are splitting off your wire to different amps. Lets look at the size wiring you would need.
Using
https://www.wirebarn.com/Wire-Calculator-_ep_41.html
At our 12 volts, 6000 watts equates to 500 amps. So if we look at the following gauges your drop in voltage would be:
4 = 1.25 volt drop
2 = .8 volt drop
1 = .72 volt drop
0 (1/0) = .5 volt drop
00 (2/0) = .4 volt drop
At our 13.8 "normal" voltage, we need 429 amps to get the same 6000 watts. So the change in wiring would be :
4 = 1.1 volt drop
2 = .7 volt drop
1 = .64 volt drop
0 = .43 volt drop
00 = .34 volt drop
These are significant drops and will likely heat up your wires and burn them. You can play with that calculator and see what you can do about increasing the number of wires to get your amperage going.
If you are running multiple amplifiers you will be able to get more wires to run them each on their own. But this is a massive under taking.
We didn't even consider the efficiency of the amplifiers here. Older amplifiers were only 50% efficient so if you were putting out 6000 watts you had to send them 12000 watts worth of power. They would put off 6000 watts of heat and 6000 watts of audio energy. I believe even if you get the very expensive, very efficient amplifiers they are still only 90% efficient which means your still up closer to 7000 watts.
If you are truly putting out 6000 watts with the most efficient amplifiers out there you need to be running somewhere around 3 alternators with one for your truck and the other two running your audio system. And each would require 2 2/0 wires to properly power up your amplifier. Assuming 300 amp alternators. And they won't use the 13.8 voltage so your 12 volt figures would be the correct ones to use.
If you are running a single alternator and the truck is dialing down its voltage then you have no where near 6000 watts in your truck and your alternator is doing its job properly.
I am running around 2000 watts in my truck. With high quality amps. I have 1/0 wires running to them and have it engineered for a minimal voltage drop. I have a cheap 350 amp alternator in as the second alternator and a second battery. This second alternator is running at full speed all of the time. My main alternator and battery run the rest of the truck and will operate as intended. The bracket cost me $300. I took out the power tap that was there and install my ground wires to the block that held it. The power tap I am talking about was where the Alternator was connected to the original power wire. I have replaced the alternator wire with a 1/0 wire directly to the battery. A bit of overkill but you can never have too big a wire. My amplifiers are 25 years old and are not regulated so they will benefit from the higher voltage. They also don't have the large capacitors in the prestage but with the large wiring and a good quality AGM battery my subs still hit hard as heck. Enough that change won't stay on the hood for long.
Good luck.