Can I specify a different bank account for the Transaction Fee to debit from as the property manager/owner?

Yes, if you are not using Master Settings then on the Property record under the Transaction Fee Option, on the "5. Bank Account" tab, you can select the option to use a different bank account to debit the transaction fee, if you pay 50% or 100% of the transaction fee option.
 
If you are using Master Settings on the Billing tab you can adjust the Transaction Fee option based on your preference, which will apply to any properties that have the Transaction Fee Option set to Use Master Settings on the "5. Bank Account" tab of the property.

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