I have no proof for this sevara, but was thinking that perhaps the mitzvah of sefiras ha'omer is example of what the Rogatchover calls a "peulah ha'nimshechet" (for examples of a peulah ha'nimshechet and an attempt to better define that term, see this previous post). In other words, the mitzvah is not simply for the gavra to count the day, but the mitzvah is for each moment of the day to be in a state of having been counted through the designation made at the beginning of the day. I think this sevara can help explain why the minhag is not to daven ma'ariv early on leil Shavuos. The Netzi"v in this week's parsha justifies the minhag based on the Torah using the term "etzem hayom hazeh", this specific day, in connection with the timing of Shavuos. I would like to suggest that if sefirah is a peulah hanimshechet, it means each moment of each day, through the completion of all 49 days, must undergo being counted. If one cuts short the last day, the peulah hanimshechet has not run to completion.
Not sure if this is right - feedback welcome.