In order to be "unobstructed" without question, the plate must be visible through the entire 180 degree range from 90 degrees to the right side viewed straight in line with the end of the plate (the fact that you inherently cannot read the numbers from the end of the plate is immaterial) to 90 degrees to the left side viewed straight in line with the end of the plate, and throughout all of these angles all the way from the ant's-eye view to the bird's-eye view - a complete hemisphere centered on the plate - and it has to be true through the entire plausible range of suspension travel. If it is obstructed ANYwhere in this range by ANYthing that is attached to the bike, then you are open to this charge. There is inherently a grey area because when you approach 90 degrees to the side of the vehicle/plate, the plate inherently cannot be read, which means somewhere there is a threshold beyond which the angle doesn't matter ... but that number is not written into law, so we have to assume the worst case, which is 90 degrees to the side.
Parts of the bike other than parts that came with the bike as original from the factory (e.g. the legally-required license plate lamp), can't be limiting factors.
In your situation, the license plate is obstructed at various positions by:
- Passenger footpegs from both left and right sides at about a 45-ish degree angle off to either side;
- The tire, when viewed from directly behind at the same height as the plate or lower and particularly when you account for suspension compression, as others have already mentioned;
- The muffler and tail section of the bike, when viewed from directly behind above a certain angle.
If the license plate is installed at the rearmost position on the bike - the stock location - then it is visible throughout the entire hemisphere of viewing angles to the back regardless of suspension travel. The bike or its attachments are not the limiting factors to plate visibility - only the plate itself is. That's the way it has to be, to fully comply with the plate visibility requirements, and that's the way your bike came from the factory.
If you put it back to stock location and present evidence of having done so at your first-attendance meeting with the prosecutor, it is not uncommon for this charge to be dropped. But the court does not HAVE to drop it. At the time that the officer observed your bike on the road, you were guilty of the charge!
If you present a lot of technical evidence that your plate is visible from sufficient angles (and no one defines what this is) then they MAY drop the charge.
The fact that you bought the bike like this is immaterial. That someone wrote up a safety certificate for it in this condition doesn't matter, either. You can get a safety inspection written up for a vehicle with no license plate at all. If you are putting a vehicle on the road that was previously unfit / unplated, that's the way the inspection is gonna be.