something being a basenote, that does not mean that you won't smell it in the top. most basenotes do. being a basenote means that the molecular size is large, which in turn means the evaporation process takes longer. they just last longer, that's all. however, i have noticed with some musks (the largest of them all, on the border of our odor threshold) that they seem to get more intense over time. (btw, often materials do smell different after some time, certainly with naturals, which consist of top-heart-and-basenotes all by themselves.)
but, think about it, if you would open a bottle of pure civet, would you expect it not have a smell for some hours?
of course, topnotes and modifiers (heartnotes) can act as a mask, covering up something in the base that then only seems to occur with time. but that's not usually how perfumers think. they rather extend something from top-to-base, maybe only trying to cover up certain unwanted aspects (a practice much more common in functional perfumery, trying to hide the bad odor of the product itself) that certain aroma materials have as a byproduct, adding something up top that seems to overpower the (often more quiet) basenotes but really rather connects to it, extend, enrich, etc.
civet has by nature (and this includes civet chemicals) a very, very strong odor, and very outspoken. so if there is a lot of it in a formula, chances are more than a little than you are going to smell it straight away.
i hope this answers you question.