Hi there.
1. Yes, the OBD port is the same for logging and flashing. You should not be in test mode for logging. Test mode is only for reflashing a map.
2. The e-tuner would send you a map and then you would decide if you wanted to flash it as "reflash" or "realtime". You should always reflash the map that has all the changes necessary for your tune/mods. Flashing via real-time only changes a small subset of the most frequently tuned tables (boost, timing, fuel). That is, it overrides the reflash for those 10 or so tables. So, it is generally used when you want to temporarily run a different map for a specific reason, such as the fuel economy map, anti-theft map, etc. The real-time map changes will remain until you reflash another map or disconnect the battery. You do not have to be in test mode to flash via real-time.
Bill