How to charge deal legal fees to a portfolio company - for a standard equity investment

It is common for VCs to charge portfolio companies for legal fees associated with a deal, up to a cap specified in the term sheet. This practice is typically agreed upon in the terms, and after the investment is complete, a bill is submitted to the company for reimbursement according to the agreement. However, it is uncommon to charge for due diligence fees, such as a software audit.