Yes, there is a workaround to avoid fund transfer fees when depositing funds to your Netbank account.
Using ShopeePay - Fund your ShopeePay using your BPI or Unionbank account. You can transfer the money to your Netbank account using Instapay for free.
Seabank - You can fund your Netbank account for free using InstaPay.
Using CIMB and GCash- Fund your CIMB account using GCash GSave then transfer the funds to your Netbank account using InstaPay for free.