It appears the FSDO is mixing apples and oranges.
101.41 applies to hobbyists
107.41 applies to UAS operations for hire or compensation.
By virtue of you filing application for an airspace authorization via the web site, the ATC facility WILL be notified. No need to call them directly. If you are going to operate for hire per 107.41, you must comply with the rule, obtain an airspace authorization and be patient with the backlog. You could call your elected official if you feel the timeframe for authorization is unacceptable to you. Good Luck!