Does a Motion to Compel arbitration have to be in lieu of an answer to avoid waiver in Florida?

In short, the answer to your question is yes.  Requesting arbitration would challenge the jurisdiction of the present forum.  If a party fails to challenge jurisdiction upon the first substantive response to a complaint the opposing party would likely claim you have waived your right to request arbitration.  All of this is depenedent upon whether the contract at issue calls for arbitration.