If the replaced speakers in turn blow the amp or APIM, sure. But the "The Warranty" isn't a monolithic coverage that gets voided for the entirety of the vehicle the second you put an aftermarket component in.
There isn't an integrated way to view the HVB charge level. Some diagnostic hardware can report the HVB charge value. And no need to charge the HVB; that's all managed automatically.
Ford's OEM version is just a branded version of the Bakflip MX4. It is not designed to be totally waterproof; Ford has issued SSMs explicitly stating that.
As long as the truck is in its fully started state then, yes, it should automatically start the engine to recharge the HVB as needed.
There isn't a dedicated bus for supplemental loads. The DC-DC converter is connected via a short cable to the lower part of the underhood High Power Junction...
Looking at the circuit and operation description the moonroof is a pretty self-contained system; it doesn't have any sort of communication bus connections. The switch just grounds either open or close trigger terminals on the motor assembly/module. The motor/module assembly is on the Accessory...
The moon roof should be able to close via remote if it can open that way. I don't have a moonroof on my Maverick so I can't say, but on the Fusion I had it vented and closed via the key along with the windows.
There may be some code for it for another model, but at least as far as the wiring diagram for the Maverick indicates the power sliding window operation circuit is pretty analog and has no module control.
Vehicles with remote start have a separate Remote Transceiver Module that receives the fob commands and Intellikey information and passes them via LIN/CAN to the BCM. On non-remote start vehicles the BCM receives and processes directly. The service manual doesn't specify directly, but suggests...
In my experience it did not. That in concert with changing battery desired charge level always resulted in a ~15.1v charging voltage (with doors closed, because opening doors reduces the commanded output voltage).