Howdy electric sheep and welcome to CPF,
With that setup you have tons of options, and yes, when using the 3SM pill and the extension tube you will gain twice the runtime using two 18650 batteries as opposed to using one 18650 battery with the 3SD pill.
Just be sure you have the pills clearly labeled and that you are clear as to which one does what. You do NOT want to run 2x18650 with the 3SD pill!
If size is not a factor, you will have the most options running the 3SM pill. With that you can run 2xCR123 or 2xRCR123...... or when you add the extension tube you can run 4xCR123 or 2x18650.
Enjoy your new light!