Before suggesting something: If I am not mistaken your ATR accessory has an optional component to adjust the clamping force and to keep it constant for all samples. Is your accessory equipped with this optional component (and did you use it)?

It would also be beneficial to see your spectra, also because absorbance actually cannot be measured, but is generated from the reflectance spectra by naively setting A = -log(R/R0).

Actually, since ATR has a limited penetration depth, it may well be that your surface treatment generates a surface layer different from the bulk with different thicknesses. In this case, absorbance becomes anyway a meaningless quantity, since it only makes sense when the wave properties of light do not play a role, but in layers often interference is very important... see e.g.

Article Electric field standing wave effects in internal reflection ...

Article The electric field standing wave effect in infrared transfle...

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I'm agree with Thomas. The ATR spectra should depend on the force with which you are press the samples.

About Opus functions. If you click right button near the spectrum you want to scale, then in popup menu you see the menu item Shift Curve and inside Top and Bottom items. After choosing these items, you may scale the spectrum by moving a mouse with the pressed left button. So you may "fit" one spectrum to another.

OPUS has a function of Baseline correction. Main menu Manipulate|Baseline Correction. It can subtract baseline automatically. The algorithm depends on your choice in Select Method tab (Scattering Correction and Rubberband Correction). Sometimes it works good. If not you may try Interactive mode, pressing corresponded button. You should point the points for baseline.