Do James and Angela make out or something?

Not in any version of the moovie they show on Sci Fi channel.

Of course they do - when he takes the bottle of alcohol to her room.

They start to talk about a plant in the bottle and how to get it in then how to get it out then give each other meaningful lusty looks then - end of scene - they just don't show it,

They have sex. With all the re-writes. directors & editing you may miss what leads one to that conclusion. But a the end of the film a comment from the ship's computer confirms they did the deed.

Spader & Bassett's characters are getting ready to have sex when the scene cuts to a close up of Tunney & Facinelli characters kissing. Then it jumps to a wide shot of a naked couple and from the dark skin you know it's a shot of Spader & Bassett. Or is it?

From the info on the Re-writes, Re-shoots, Editing & Deleted Scenes

When he took over the editing of the movie, Francis Ford Coppola put together the zero gravity sex scene between Angela Bassett and James Spader using out-takes of the zero gravity sex scene between Robin Tunney and Peter Facinelli that happens later in the movie, with Tunney's skin color being digitally darkened. He did this to add more to the relationship between Bassett's and Spader's characters.