Earlier quoted context omitted.
“Shadow government” = “Deep state”?
They're both somewhat vague phrases that are heavily context-dependent and have somewhat different connotations, but yes. There's nothing wrong with the phrase "deep state". If you're concerned about associations with Trump (which I think you should not be), you can use a former Obama official's favored term, "the blob". Both, and many other similar phrases, are common in the foreign policy literature. I think the fi…
"The Government" isn't really a single institution, but a surprisingly loose collection of various institutions that all have some level of momentum guiding the direction they move in. It's critical to note that these institutions may have interests that harshly conflict with one another. Even the intelligence community, insular as it is, cannot be thought of as a monolith, but as various institutions with various priorities, some which conflict with the interests of other government institutions.
When the government does something we dislike politically, or does something we don't understand, it's "the deep state" or "the shadow government" which betrays a deep misunderstanding of what the government is. There's no central, shadowy cabal controlling the affairs of "the government" from behind the scenes, the various institutions that comprise the government maintain momentum and do what is in furtherance of their particular interests.