I would be grateful for your advice.
The clause that additional expenses are to be paid, but reduced expenses are not reimbursed (as far as you quoted it, we do not know the entire contract), I find unfair. You might (with a lot of patience) find a court that follows this logic and overturns the whole provision. However, I would not take this risk ;-).
I consider it unnecessary that you should sign an additional agreement. Everything has been said. Your contractor should simply send you the invoice.
If the static calculation is to be redone, that implies to me that there is already an initial calculation. Why should it be recalculated?
Conclusion: In all likelihood, you will have to pay for the additional gravel. That is completely normal. Whether the additional effort is correct cannot be assessed by us. Get an independent construction supervision that checks these matters and advises you (commissioned by you, paid by you).
Regarding the static calculation, it depends ... why, how, what for?
For future builders: The service specification underlying the contract for work (construction and service description) should always be read and understood very carefully. Before signing. Generally, external expert knowledge is required for this, which the builder should additionally and independently purchase from someone other than their contract partner.
In addition to the "construction-related" review of the service specification, a (separate) legal review of the contract for work is also advisable.