Well... I believe the base of the antenna should be on a metal surface with the top of the antenna being parallel to and having a clear view of the sky. That is, the antenna can NOT be mounted where the signal from the sats must pass through anything except glass to reach the antenna.
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Yes it can be installed in any direction, so long as the bottom of the antenna is on some metal surface. Its best to just use the 3x3 magnetic pad that comes with it.
You can also mount the antenna underneath your dash. Just make sure that its on the pad and that there is no metal above it. Glass and plastic are fine and won't interfere with the signal, but metal will.
If you do this, before you finish your installation go to 'Hardware info' -> 'Connection status' and check your signal strength.
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GPS signals need line of sight to the satellite, so positioning the antenna on top of the aircraft maximizes the satellites that can be seen and minimizes multipathing, and also gives some protection to ground based interference/jamming.
Not listed in the CAE but there are some advantages in not having critical cables running half the length of the aircraft, so the location may be the one that got a cheap, simple and easy to install and test location for the antenna, and per below it may not make a difference for this particular nav system.
Keeping the antenna near the C of G has two two effects, the first is that it means the position output is near the actual aircraft center, avoiding issues with systems having it off the side of the taxiway or showing altitude while still on the runway. There are also several effects the reduce the precision if there is rapid motion of the antenna during fixing, so a central location will get more accurate position. All of this can be 'solved' with software, but does make accurate GPS dependent on accurate pitch/roll information (and good software). Presumably in this case software was traded against the other effects of central location to produce the current placement.
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