When you submit your tender do you include clarifications / qualifications & exclusions?
It’s important to include these as this clearly sets out the parameters of your bid. What’s more important however is that these are carried through to the subcontract. The main contractor may use your price breakdown as the contract sum analysis but generally will leave the rest of your bid.
If you don’t include your clarifications / qualifications & exclusions, they won’t be contract documents & so won’t exist. When pricing ensure that you price what the tender asks for, if something is missing include under one of the above headings, this ensures your price is comparable against others, clearly identifies that you’ve read & understood the brief & gives values for the missing / additional items required.
Always price the project properly, ensure that your rates, prelims, programme etc reflect the work & conditions, but by breaking down your price in this way may give you the opportunity to explain to the QS why your price is more expensive, rather than being cut as being too high on the first review.
If after that your price is still too for them, so be it. You’ve priced it correctly; do you really want to take on loss making work?