My question is this, if you have migrated to FLAC/ Rocbox/ iPod combination how (if at all) will it affect the connectivity to car audio head units (that support iPod connectivity) via the bottom connector (not sure of its real name) on the iPod ?? Will the control and connectivity features still work since the iPod's native firmware is being replaced with Rockbox?

Most likely they won't ... Rockbox is a file-system browser firmware whereas the original apple firmware maintains a specific database system that can be read by ipod-compatible headunits to e.g. display tags.

on the other hand, you could use your rockboxed ipod as any usb mass storage if your headunit supports it.

Yeah, they won't work. Those units are meant to work with the iPod's default firmware. Rockbox doesn't replace the iPod's firmware but it is an alternative that is installed on the iPod. It is kinda like having two OS's on a computer. Rockbox can send audio out through the iPod's headphone adapter and through the dock connector (the name for the plug on the bottom of the iPod). However, any car head unit that has iPod connectivity (and thus can control the iPod and display information) simply won't work as it uses the iPod's default firmware.

You do have other options though. As JeanLuc stated, you can get a car CD deck that is compatible with USB storage devices. The deck will have to play FLAC files though and that might be a problem. Or you can get a car CD deck that has a auxiliary audio input and use the iPod and Rockbox to play the FLAC files, the iPod will control everything.

Rockbox maintains a database equivalent to the Apple one.

The reason headunits don't work is because they communicate over the serial port and no one has figured out the details for how the Ipod's serial port works on the newer ipods.