Is it permissible for a contracting company to raise the price of raw materials in the quotation above the market price as a precaution for future needs, and is it permissible to take the difference in price between what manufacturers pay and the market price set for the client?

The answer depends on the nature of the contract between your company and the project owner. If the contract specifies the price of raw materials separately and you have been entrusted with determining the market price, then it is not permissible to increase it. However, if the contract is for the total value of the project, or an absolute sale of raw materials by the company with a separate agreement for labor, then there is no harm in setting the value of the raw materials by agreement with the project owner, regardless of the market price. Similarly, an agreement can be reached with the workers on the wage amount without informing the project owner, unless you have been entrusted with that, in which case lying is not permissible. The way out is to agree on a total value for projects without detailing the costs.