The etymology of this is very clear. "A body that emanates (or has emanated)."
As the balance of citations reveals, sprul pa'i sku is used much more often in a general sense to refer to an "incarnation" than to the emanation body specifically of a buddha. In most cases, the term has connotations of wonder, respect, and high levels of spiritual attainment, and is often used in contexts where an individual proves his status through a supernatural act like floating in the air or increasing the yield of grain for a given year, after which people invariably say, "He must be an incarnation." If we compare this term and usage to the more value-neutral term "skye ba," which is also translated as "incarnation" and used throughout the Blue Annals to establish identities and lineages, it is clear that "incarnation" in the form of sprul pa'i sku carries some of the loftier connotations of its other definition and confers an intentionality and reverence upon the otherwise undesirable phenomenon of rebirth.
The "emanation body" definition is used sparingly in the Blue Annals, despite it being the first definition in the bod rgya. This is certainly because the Blue Annals doesn't concern itself as much with the stories surrounding buddhas, and thus doesn't have the opportunity to employ the term in the sense that it is preponderantly employed in other literature. There are very few cases where one could make an argument for its usage where Roerich otherwise translated "incarnation." It is interesting to note, however, in the example on page 689, that Roerich translates "incarnation" and then puts "nirmanakaya" in parantheses. For him, there is not much distinction, and a literal translation of terms supports this perspective. The patterns of usage make it clear, however, that there is indeed a distinction, with skye ba being used for basic rebirth incarnation, sprul pa'i sku being used for enlightened and/or intentional incarnation, and sprul pa'i sku being used to describe the worldly activity of buddhas.
It's worth mentioning the atypical usage of "sprul pa'i sku bsdu ba mdzad", which Roerich translated as "passed away (lit. "gathered his manifested form")" (563). The context describes the worldly death of the second Buddha, and thus "gathering the emanation body" conveys the transition from one body to the next.
Incarnation: 11
"Well, this must be an incarnation, who will become an exceptional man" (115)
"The mother then believed (the boy), and thought that he must be an incarnation." (135)
"This great paṇḍita, who was known to be an incarnation…" (164)
"this Indrabhūti, an incarnation and master of the tenth stage" (361)
"All felt amazed and thought that he must be a great incarnation." (422)
"The first incarnation series" (473)
"The present incarnated bla ma (sprul pa'i sku) rang byung kun mkhyen chos kyi rgyal po was born…" (517)
"The second incarnation series" (520)
"Before his death, he said, "This one will be an incarnation!"" and "At the age of five, he uttered many psalms of benefit to others, and it became known throughout the whole country that an incarnation (nirmāṇa kāya) had appeared." (689)
"Once he was told by some hillmen (ri pa) that an extraordinary incarnation was living at lha gdong and faith was born in him." (691)
"a ro had been an incarnation" (999)
Emanation Body: 2
"This second Buddha passed away (lit. "gathered his manifested form") on the 25th day" (563)
"the prophecy by the nirmāṇa-kāya (Vanaratna)" (817)