The petitioning employer files and pays the USCIS fees under the fee schedule; how the group allocates the cost between entities is an internal accounting matter, not an immigration one.
Petitioner pays the government; the group settles internally
Hypothetical example: a Quispamsis insurance back office and its U.S. affiliate disagree about which entity should bear the L-1B expense, since the affiliate benefits but the Canadian entity employs the analyst. The USCIS petition fee, any fraud-prevention fee and optional premium processing are set by Form G-1055 and are paid with the petition.
An intercompany recharge afterward is a matter for the finance teams and the transfer-pricing advisers, not for USCIS. What the petition must show consistently is which entity is the petitioner and which entity will supervise the work; the cost allocation should not contradict that. Additional costs to plan for include certified translations of any French-language records, the L-2 applications for family members and the eventual cost of an extension if the eighteen months become longer.