The U.S. affiliate is the petitioner and should pay the USCIS fees itself. How it prices the monitoring contract is commercial; a line item reimbursing immigration costs is not itself fatal, but a contract that treats the technologist as the client's hire is.
Price the service, not the person
The petition fees on Form G-1055 are the affiliate's obligation as the employer, and paying them from the affiliate's account keeps the employment relationship clear. Whether the affiliate recovers those costs in its contract price is a business decision, and many service contracts include mobilization costs of various kinds. The risk is not the money but the framing.
A contract that itemizes the technologist's hourly rate, requires client approval of his replacement and lets the client set his hours reads like staff augmentation, which is the labour-for-hire pattern the rule targets. A contract that prices a monitoring program with defined deliverables and includes a mobilization charge reads like a service. Keep the affiliate's professional fees, premium processing and travel as its own overhead.
Separately, confirm that the technologist's salary will be paid by the affiliate on U.S. payroll, since an employee who stays on Canadian payroll while working full time in the United States raises tax and status questions the immigration file does not answer.