Just to clarify
Carbonite BETA VERSION is the version one should be using. This is for individuals who happen across this thread that have not already upgraded and may have further questions.
To answer your first question; in short, no.
Second question; no and yes, Carbonite "docks" the minimap and manipulates it to blend in with itself.
Third question; vice-a-verse, this ties in with the above answer. The minimap blends into the view of the small Carbonite map and they essentially compliment each other.
To simply undock and make Carbonite leave the Minimap alone; Carbonite options, Maps, MiniMap tab, and uncheck Combine Blizzard Minimap with Carbonite Minimap.
Quick notes:
Carbonite may work with Gathermate, haven't checked in ages, but it already has a built in node module. Carbonite Nodes does not need to be loaded for this functionality but it is required to load Carbonites default nodes into it. This is done by going to Carbonite options, Guide & Gather, Gather tab, and importing while Carbonite Nodes is enabled in your addon list. Additionally, Carbonite has a routing function that will route all available nodes of a specific type in the zone.
As of late I've noticed Carbonite only displaying 1 quest blob and that's for the currently tracked quest. However I'm not sure if this only applies to Pandaria quests or not.
The map should already display icons regarding flightmasters, mailboxes, etc. If, like in my case, the icons are visible but only barely then you can right-click the map and go to scale.