US retail boxes have printed number of parts included in a set. For 42063 set this is 603 parts:
Bricklink is unofficial LEGO market place/catalog has 42063 set inventoried. This means this set has been taken apart, each part has been accounted and put accordingly into inventory of this set. It also contains 603 parts. There's sticker sheet in set's inventory, but this is something LEGO does too, probably since Part tab on Brickset states it has 602 parts (Brickset fetch data directly from LEGO, but sticker sheets are never included as a part). I'd like to note that set inventories are highly accurate on Bricklink as each web site member can submit change if there are errors (and this is done fairly often when inaccuracies are found). LEGO, sometimes, alter the model slightly and this is being noted with an alternative items inventory, like in the following model. With 42063 set there's no alternate inventory.
Counting all the parts used in each step of official building instructions got me 599 parts. I agree, there might be few parts I've missed, but this is number is closer to 603, than yours 550.
Part inventory at the very end of the same building instructions gave me 601 parts. Again, one or two must have been missed, but still closer to 603 than 550.
I found video review for this set (with speed build), and if you check it on exactly 9:36 you can see all the spare parts left, which are not accounted in total part count. It is just a few pieces, which means almost all of the parts are used to assemble the set.
Rebrickable also state 603 parts for the 42063 set. However I'm not sure what is the source of the part list.
I don't know any other more reputable sources than provided here. You must have made a mistake while calculating the parts.
Alternatively, I could suggest to disassemble the model entirely, with all pieces removed and then assembled back together following the building instructions mentioned above. This way you'll be sure you have complete model with no missing parts.