The problem is not in GeoSetter but in whatever created the XMP file you are using as your ACR settings.
The XMP file is data in a structured format that can be understood by computers. As XMP data is extensible - this means you can add to it without breaking it, provided it remains structured and follows certain rules - there needs to be a method of avoiding potential conflict. What happens if two applications want to add data called 'Status'. So that applications can know that this 'Status' was added by this tool and has a different mean to that 'Status' which was added by that tool something called a namespace is used. The namespace is used as a prefix to the data item, without affecting it's name e.g. this:Status and that:Status. To control namespaces they must be given a unique, within the document, definition which is usually in the format of a URL, although it does not have to be a valid one.
In the extract of your XMP file there are two namespaces defined, however they have the same prefix i.e. mediapro - the definitions are 'http://ns.microsoft.com/expressionmedia/1.0/
' and 'http://ns.iview-multimedia.com/mediapro/1.0/
'. This is something that breaks the rules of an XML document i.e. you can't re-define a namespace like this. Exiftool is correctly throwing this out as an error, although GeoSetter then allows you around this by treating it is an ignorable minor error. In fact GeoSetter is sweeping the problem under the carpet for something later down the processing line to fail.
Unfortunately when Microsoft bought iView they changed the namespace without really thinking things through. They wanted to put their mark on the software. It will be interesting to see what PhaseOne do - will they fix this or compound the problem by having a new and third namespace? The consequence of Microsoft's clumsiness is that if you had synced data to images using iView then they were stored under the 'mediapro' namespace. If you synced the data again using Expression Media the data was added again, this time under the 'expressionmedia' namespace. This duplication up of meta data isn't clever. Fortunately Expression Media was badly coded so that if you removed a catalog set and synced the meta data to the image it removed the details from both namespaces. However other software might not know that these two namespaces are 'linked' and this could lead to problems.
Anyway back to your questions:
1) Are the two 'mediapro' sections created by II a bug or intentionally ?
Neither and both! I reckon that the Camera Raw settings you are using contain more than they should. You need to edit these and remove both the iView and Expression Media details. On XP these files should be in C:\Documents and Settings\your name
\Application Data\Adobe\CameraRaw\Settings, although this may vary if you have CS4 or CS5, as Adobe might have changed locations (again!).
The XMP files should really only contain data about camera raw settings. This data is held in the 'crs' namespace, although there will be some 'rdf' data as well. Make a copy of these files before editing as if done wrong the file will become invalid. Below is an example of one of my ACR settings files. Your may vary depending on setting chosen and the version of
<x:xmpmeta xmlns:x="adobe:ns:meta/" x:xmptk="Public XMP Toolkit Core 3.5">
2) Is there any way two keep both entries when using GeoSetter ?
You don't need or want both entries in the ACR settings files. ImageIngester will add this data as appropriate. However I'm not sure how ImageIngester knows which namespace to use - seems to always use the iView namespace for my ingestions and I don't know whether this is hard-wired in ImageIngester or is a setting that I can't trace.
3) What would be the consequences of having just one left after GeoSetter invocation ?
If you do as suggested for question 1 then you should only have one of these sections of data - and GeoSetter, or actually ExifTool, won't complain.
Hope this helps.