A: Yes. If it says you need a Phaser, the Enterprise, a Computer, a Malfunction, a Transporter, Romulans, or Worf, then any deck’s version of that card will do, regardless of the image.

Also note that Holodecks are interchangeable with the Holosuite; similarly, the Runabout counts as a Shuttlecraft and vice versa.

This also applies to other decks you might combine:
Milk in Fluxx 5.0/SE/Remixx = Milk in Drinking Fluxx
The Brain in Fluxx 5.0/SE/Remixx = Brains in Zombie Fluxx
The Sun in Fluxx 5.0/SE/Remixx = Sunshine in Nature Fluxx
The Castle in Fantasy Fluxx = The Castle in Fairytale Fluxx
The River in Camping Fluxx = The River in Hundred Acre Woods Fluxx

we’d probably even say:
Trees in Nature Fluxx = The Woods in Fairytale Fluxx
The Dwarves in Fairytale Fluxx = The Dwarf in Fantasy Fluxx

It’s always good practice, when combining decks, to compare the Keeper sets, and decide which cards you are going to consider to be equivalent, and, like any house rule, make sure everyone knows how those are going to work.