Those are a great set of spectra. I’ve also chased some objects to very low altitude. While you don’t get anything like the quality, you can still get enough photons for some useful data.
To avoid any confusion on the atmospheric response correction, it is not supposed to get rid of the telluric lines. These are the sharp lines and absorption bands due to water and molecular oxygen. They are harder to get rid of, and while there are ways to do it, typically they are left in spectra unless they need to be removed for measurement purposes. They can actually be useful when submitting spectra to databases as they give anyone who then downloads the spectra the ability to redo the wavelength calibration, using the same approach for spectra taken by different observers.
The atmospheric correction removes the continuous transmission/absorption component across the whole spectrum. I could be wrong, but I think this is due to Rayleigh scattering in the Earth’s atmosphere. The same affect that gives the sky its blue colour in daytime and makes the Sun look red when it is near the horizon. When you correct for this in a spectrum, your response correction curve should be very smooth. See the below plots of a low resolution wide wavelength range response correction curve, and a narrow range high resolution curve.
Let me know if you need any pointers on database submission.