Hi Wesley,
Can you post a small org file that reproduces these problems? Without looking at the entire file it's hard to figure out what's going on.
For example, AFAIK the {{{date}}} macro does not magically expand the current date, rather it refers to the #+DATE property of the document. If this is for some reason not included in your standalone export command, maybe this is the reason why it's not being expanded.
As for the others, I think orgXXXXX is the default auto-generated reference format, so my guess would be that something else in your main Emacs config is enabling the human-readable labels, and which is not being loaded in the script command. I do not really understand the third point about the periods. Again, a self-contained example would help.
Best,
--Diego