"The Bayer CFA is transparent to IR"? Do you mean "Bayer CFA does not detect IR"? Most cameras have IR-blocking filters between light and sensor.
With these heavy ND filters, the exposure level for the visible spectrum must be increased to achieve an adequate exposure, usually with longer exposure times. But since the IR in some of those filters is not attenuated as much as the visible spectrum, the IR weighs in heavier in the total exposure.
It is true that most cameras use an IR absorption filter in front of the sensor, but it is not an absolute blocking or hot-mirror filter, so there is still some IR coming through. The relatively elevated IR contribution is reduced, but not totally absent.
With that relatively IR rich spectrum (the balance is skewed despite the IR filter, otherwise it would be even lower), the color dyes of the Bayer CFA (which are transparent for IR) will not prevent to record an elevated signal level in all RGB filtered channels, coming from a different (IR) spectral band.
Hope that's a bit clearer.
The Lee glass filters are supposed to use materials that also attenuate the IR part of the spectrum. So while there is a shift in overall color balance, it can be corrected with a shift in color temperature.