For glass of say 2mm thickness, you can neglect the reflected light as it is negligible. However, it depends upon the quality/purity of glass and hence thickness.
As you speak about transparent thin film on glass: Can you please tell me which type of film you have? What material and method is used to prepare this film.
Normally, it is this film/material that absorbs more light for transparent films than the standard glass substrat/support.
The Geometry can be determined from the instrument itself.
Nevertheless, I recommend you to use T spectra instead of R. Since your film is transparent there should not be more problem to determine the refractive index, absorption coefficient and average thickness of the film.
For this you can use the Envelope or PUMA methods. Also, the reflectance and absorbance of the substrate matters a lot, so depending if you are determining this parameters near the fundamental absorption region or not you will need to take into account the refractive index of the substrate or even the absorbance of the substrate.
If you have any further questions please don't hesitate.
The effect from the glass in your case is only negligible if you don't need high resolution and are in a range of the light spectrum where the absorption (and reflectivity) of your film is much larger than the one from the glass material.
For example, in a typical glass window (the one for buildings/houses) the transmittance is about 96%. There are 4% losses (via surface reflection and absorption). Also this is in the visible. In the UV glass is very absorbing...
From what I see your film is actually very absorbing to apply a single measurement method to determine the absorption coefficient accurately. If you can measure both R and T (and the optical parameters of the substrate are known) your problem is solved. Since you will need to solve a system of equations in order to get "n" and "alpha" from T and R for all the spectrum.
Another tactic is to measure R or T twice with different incident angles, then you must solve again a system of equations. There are several ways. Still you can apply the Envelope method, but since you only have 2 interference fringes in your spectrum and the amplitude is shrink due to the absorption of the film (or due to the similitude between the refractive index of your substrate and film) it may not give you accurate results.
Concerning the effect of the substrate you can check the following work:
Influence of Substrate Absorption on the Optical and Geometrical Characterization of Thin Dielectric Films, Applied Optics, Vol. 41, Issue 34, pp. 7300-7308 (2002)
"The role played by a glass substrate on the accurate determination of the optical constants and the thickness of a thin dielectric film deposited on it, when well-known envelope methods are used, is discussed..."
PS: If you send me the T files of the substrate and film I can try and run it here. I don't need to know what material is or any other information concerning the optical properties of the films.