External power with usb data+/-

I am building my own Arduino board for use in a custom project for my car. The question I have relates to using a power supply for the microcontroller (a Atmega328) while simultaneously outputing signals on the USB Data+/- lines to a laptop.

Here are the devices for this problem: Atmega328, FTDI chip, 12V ->5V Buck converter, laptop computer.

I will use this board in two types of scenarios.

Scenario A (Initial setup and configuration/validation): Connect the USB from the laptop to the USB on the board, draw power from the USB +5V pin. Communicate to the Atmega328 through the serial->USB hardware (Serial.print(?)). In this setup the 5V buck converter is disconnected.

Scenario B (Debugging/reprogramming): Board is installed in my vehicle. Draw power from onboard 5V buck converter (which is connecte to the car battery). Connect laptop USB to board USB so I can transmit/receive Serial.print(?) messages or program. No power is needed from laptop USB, but USB Data+/- is needed.

Scenario A is easy, I know that will work.

But there are some concerns/unknowns for scenario B. My original plan (for scenario B) is to make USB GND the same as the GND on the 5V buck converter. The Atmega382 and FTDI chip will still be powered by the 5V buck converter, but the USB +5V pin will be disconnected via jumper or slider. This means when the board is installed in the vehicle the USB GND will be the same as the car battery GND. Will the FTDI be able to output signals to my laptop USB Data+/- with the USB +5V pin disconnected?

For scenario B my car battery, custom arduino board, and laptop battery all will share the same ground. Will this cause problems? What about if I decide to plugin my laptop to the wall? Now car battery ground is connected to ground in my home. I worry about potential differences causing power to flow through my laptop causing my laptop to fry.

Has anyone tried this?

I've been studying the reference designs on the hardware page to see how they handle simultaneous input from VIN and USB. Looks like they shut off the USB 5V whenever VIN > 3.0 V. Using my Duemilanove I tested if Serial.print would still transmit on the USB data +/- with the USB +5V disconnected and everything still seems to work ok. I'll verify when I get the board made, but it looks like my original plan is safe.

Btw, I tested this with my laptop plugged in to the wall using a 12V external power source to VIN.