Yes.
Entrenchment is a good add on, it adds a lot of defensive capabilities (e.g starbases) and allows you to upgrade normal sins defences. (e.g your planets arn't wide open to defeat if your fleet is destroyed - it gives you time to rebuild).
If you buy both you can choose to play either vanilla (normal) Sins of a Solar Empire or Entrenchment (They both now work as seperate as you probably already know) - I would assume their would be a seperate one for the new expansion pack, however with it being Diplomatic i believe it would then (possibly) become part of both vanilla sins and entrenchment. (Unless they made an option so that when you click on you had an option e.g play as part of entrenchment/vanilla etc).
As you can download them on impulse you don't have to worry if you loose your game, however in the future they may be cheaper (but if they are bundled retail - it may cost more due to distribution costs and retail markup etc).
About tokens, i have no idea, unless their is a discount code, but i do not believe there is.
Hope this helps. 
