> I have been using [a calibrated] scanner as a densitometer ... then I started experiments
> with tanning and staining developers ... all my readings were off ...
Sensitometery/densitometry for printing negatives developed with staining developers is, as you have stated, a can of worms: extra large, extra wiggly and extra slimy worms, all in an extra large can.
B&W densitometery makes the assumption that the negative attenuates all wavelengths of light equally. For most black and white films this is a valid assumption. The reading offsets caused by the spectral variations of the densitometer light source, the densitometer sensor response, the enlarger light source and the paper spectral response can all be corrected for with a linear calibration factor - and/or all come out in the calibration process.
Color densitometry - for color printing - works by matching the color filters in the densitometer to the spectral sensitivity of the dyes in the color emulsion. Color densitometers are made for a specific mini-lab or process. They come with filters that are specific for the materials used by the laboratory and with a light source that mimics the light source used in the printing machine. They are designed to read quality control strips where there is a nice big patch of even density to read.
Color densitometers for graphic arts use are matched to RGB separation filters and CMYK printing inks. Again, they read QC patches or the patch left behind by imaging a step tablet.
UV densitometers are designed for graphic arts work with mercury/metal halide UV light sources and polymer/gum emulsions.
Densitometers use a diffuse light source for transmission and an off-axis light source for reflection: both are specified in ANSI/ISO standards. These standards are designed for use in graphic arts/printing but are often used in color densitometers for mini-lab use simply because they provide some interoperability.
Densitometers are _not_ designed for use in conventional darkrooms. However, for black and white work with regular silver processes they work well enough to be useful. For alt-process work densitometers must be used as they are the only game in town. UV graphic arts densitometers work well with many UV sensitive alternative materials.
Scanners are even further removed from darkroom applications, though if used with the most conventional of black & white materials and processes it is possible to calibrate them so useful results can be obtained.
The proper instruments to use in a traditional enlarger-based darkroom are color analyzers and enlarging meters.
By working under the enlarger they automatically take into account the effect of Callier effects from condenser and diffusion light sources, flare and stray light of the enlarger. Many of the spectral effects of the light source are accounted for in the calibration.
The measuring spot of an analyzer or meter is small enough to read millimeter sized highlights. The same highlights on the negative are only a few hundreds of microns across and can't be read with a bench densitometer.
A color analyzer will compensate for the spectrum of the enlarger light source because it has filters that match the sensitivity of the color emulsions in the paper. An enlarging meter will compensate for the enlarger's lamp spectrum with a constant calibration factor: it either comes out in the individual calibration of a meter and enlarger or can be added to a supplied calibration developed on a different enlarger.
The premise of all this goes straight out the window when staining developers are used.
Conversely to black and white work, the color of the negative now comes into play - and it interacts with the spectra of the light source, the color response of the measuring instrument, the spectral sensitivity of the paper, any contrast filtration, and the effect of spectrum on multi-grade papers.
Conversely to color work, the color response of the densitometer is not matched to the color response of the paper. Some users of graded paper have had limited success using the blue channel of a color densitometer (yellow channel on a color analyzer) to read pyro negatives.
An enlarging meter can be used with staining developers, but the methods needed are different from those used with conventional negatives. The stain produced is proportional to silver density and so a multiplicative correction factor is needed: the meter reads a density of 2 stops (0.6 OD) but the paper may see this as a density 1.5 times higher at 3 stops (0.9 OD). Changes to the lens aperture or the enlarging height, however, are seen the same by the paper and the meter.
For this reason, a meter needs to be used first in absolute mode to read the illumination of the negative's B+F (no stain) on the easel to take into account light source intensity, lens aperture, enlarging ratio and negative base density. The meter is then used in density mode to determine paper grade, exposure needed to bring the low values (shadows) to the desired density and the exposures needed for burning and dodging.
The Darkroom Automation meter (disclaimer: I own the company that makes Darkroom Automation products) will work in absolute/density mode. However, in my experience, the calibration procedures for using the meter with pyro in combination with MG paper may not be worth it for most casual pyro printers - it is often easier to make the usual split grade printing double test print.