The answer in short is yes, you can Harbalize individual instruments but the references supplied with the product will be of no use for this purpose, basically because the spectrum with an individual instrument will generally be narrower and confined to a more limited range. That being said you can still use it to alter the sounds of individual instruments to taste.
Whether you will get substantially better results that way is debatable, basically because it is hard to know how it should be altered to give the desired end result when the instruments haven’t been combined yet. What I would argue though, is that it would definitely be beneficial to use the spectrum analysis results of a given mix down to verify that it is well put together and if not make adjustments to your mixer settings to get the right general form for the final mix down.
Once you’ve tweaked it as best you can you can then use a Har-Bal filter to apply the final polish to the mix.