How do I reflect the fees on Form 8949 for ETFs which held actual precious metal commodities (e.g. PALL, PPLT, GLDM)?

As it appears these fees are a type of management fee, such fees cannot be deducted.  The management fees you paid in connection with owning these precious metal ETFs are akin to miscellaneous investment related expenses, and a result of the Tax Cut and Jobs Act, are no longer deductible.  Miscellaneous investment related expenses include such things as fees for investment advice, IRA custodial fees, and accounting costs necessary to produce or collect taxable income.  

In contrast to management fees, is investment interest expenses.  Investment interest expenses represent the interest paid on money borrowed to purchase taxable investments and is deductible but only if, among other things, the taxpayer itemizes deductions.  

Also, the sale of the underlying commodity by the ETF to cover fees may affect your basis in the ETF.  Moreover, if the ETF sells a pro-rata amount of the underlying commodity to cover fees, each shareholder may have a gain or loss to report.  Such gains/loss may be reported separately to each shareholder and thus will not be reflected on your 1099-B.