A number of reasons are given for sending away the mother bird before taking her eggs/young. The Rambam says it is for the mercy on the mother bird. The Ramban says it is to perfect our own mercy.
Contemporary halachos seem to ignore the spirit of this mitzva. From Star-K:
Once the mother bird has flown away, one must take the eggs or chicks. Even if the mother bird is watching, one still fulfills the mitzvah. To perform a halachic acquisition, they should be lifted to a height of three tefachim (about 12 inches). Upon completion of the mitzvah, one may put back the eggs or chicks and need not keep them.
After one takes the eggs or chicks, they may be declared hefker by the one who acquired them and then returned to the nest. After the mother bird returns, another person may fulfill the mitzvah. In this way, the same nest may be used over and over again.
The structure of sending the mother bird away without needing the eggs (and returning it to send the mother away again) seems antithetical to both reasons stated above. A footnote to the latter paragraph drives this contradiction home:
If the eggs cool down too many times, they may no longer be viable (University of Arkansas Division of Agriculture). The mitzvah is not fulfilled on non-viable eggs.
Does the halacha go by a different reasoning? Do we ignore any reasons when performing the mitzva (as in Brachos 5:3)? Is the Star-K promoting structure over spirit?