Does this price include "E-File"? And, if I pay now, can I decide later how I want to file, i.e., separately, jointly or combined, etc?

Any online software includes e-filing.  The fees are for using the software, and they are the same whether you e-file or mail the return in an envelope.

If you decide to file married filing separately that means TWO returns--one for each spouse--and two fees.  Married filing jointly is one return/one fee.