ATR spectra are absorbance data from a thin layer near the surface of the ATR crystal. Penetration depth depends on frequence and that can make them look slightly different. Surface can be slightly different in orientation and composition than bulk. Not much you can do to change that.

It is possible to fully correct ATR spectra, see, e.g., Article Sophisticated Attenuated Total Reflection Correction Within ...

However, you have to keep in mind that there is, strictly speaking, no such thing as IR-absorbance (FT is just a recording technique). What you probably mean are transmittance-absorbance spectra (-log10T), but those do also not reflect (no pun intended... ;-) IR-absorbance. Instead you have to determine the absorption index function (the imaginary part of the complex refractive index function) to obtain the true absorbance, see, e.g., Article Understanding the Limits of the Bouguer-Beer-Lambert Law

Article The Bouguer‐Beer‐Lambert Law: Shining Light on the Obscure