For a planet which has a temperature gradient, hot in the center and cooler on the surface, why do we get absorption lines? For a planet which has a temperature gradient, hot in the center and cooler on the surface, why do we see absorption lines?
Similarly, why do we see emission lines if the planet  is hot on the surface and gets cooler as you move to the center?
Note, for this question I am only thinking of the planet as a black body, not as something, for example, transiting a star and observing the spectra (transit spectra) of the light that shines through the planet's atmosphere. The source of the spectra is the planet itself.
 A: 
For a planet which has a temperature gradient, hot in the center and cooler on the surface, why do we see absorption lines?

The hot center sends photons  within the black body spectrum with appropriate energies to excite surface cold atoms ,so the black body curve will have holes, where energy of the photons has been absorbed in exciting surface molecules.

Similarly, why do we see emission lines if the planet is hot on the surface and gets cooler as you move to the center?

The black body spectrum is a continuous spectrum from thermal excitations. There exists though a probability that from the high energy tail of the black body energy spectrum  , electrons from atoms on the surface are taken to a higher energy level and then relax back to the ground state emitting the specific line of that atom. 
A: Well...there are several possible things which look a little strange with your question, but in general, emission occurs in hot regions and absorption occurs in cold. So, your "planet" could be emitting (presumably thermally, unless it's actually a star...) from the center and that blackbody spectrum is being absorbed by the cooler atmosphere. This is exactly what happens in stars.
The reverse is easier - if you have a planet which is somehow hotter on its surface (mercury might be an example, but again there are more significant physical processes going on), the surface would be emitting as a blackbody, or with spectral lines, or however you like.
