No. Unfortunately, we cannot take the fee directly from the incoming deposit. However, we have introduced an option for these situations with the 24.05 CU*BASE release.
In the ACH On-Demand Posting Configuration, you may uncheck the Base deposit (seq 99) suffix must have sufficient funds for fee in advance, without the incoming deposit checkbox to skip available funds verification when the base deposit (99) account (which must be a savings/checking account) is chosen as the fee account. If this option is configured, these accounts have the potential of going below available/negative from the fee, but it creates the opportunity to pay the fee using the incoming deposit funds if there are sufficient funds left over after all the distributions have been posted.