I might have overlooked them but I couldn't find any spacer pegs in my transport. it seems to fit okay not sure why they are needed

I think that they must have decided not to include them but not updated the paperwork. I'm pretty sure that the spacer pegs were left out on a mass scale. I didn't get them either. I think they will be useful if you are fielding multiple huge ships, so that they are at different heights.

There were no spacers with my transport, and it does not seem to need them. I agree I think they didn't update their paperwork.