The issue
I got to the point in my build when its time to attach the Y axis to the frame and noticed something very off between the guide and my build.My Y axis was a fair bit shorter then the one shown in the guide, which meant if I had the motor at the back, as per the guide, I would lose a fair amount of print area.
Why
Looking around the forums I noticed I wasn't the only one with the issue and it was caused by a difference between the official github and the wiki.The wiki stating 370mm smooth rods with threaded rod to match and the github stating 405mm smooth rods and threaded rod to match.
The difference (35mm) is roughly the size of the mounted Y axis motor and the print area lost if mounted at the back.
Semi-fix
Move the motor to the front, remove the washer and nut from the idler side and move the belt tensioner on the bed plate.Moving the motor to the front gains a few cm's, removing the extra bolt and washer gains roughly 1 cm and moving the belt tensioner should regain the last few cm/mm.
Dragonfly DIY's blog outlines the changes.
Its still not ideal however as its its re-drilling the print bed wood, removes the supporting washer holding the Y axis to the frame, doesn't look as clean (you have wires going from the very front to the back along the Y axis) and leaves little room for error/tweaking.
As I've already got the correct length threaded and smooth rod on hand from my original Prusa I will order some more GT2 belt (2m so I have some spare) and will re-build the Y axis later.
For the time being however 150x200x200 (mm of course) should be enough to allow me print some basic things to improve my setup (RAMPS mount, RasPi mount, auto bed levelling parts and spool holder)