This is definitely a situation where you need to engage a very good painter/finisher.

They can work miracles in these type of scenarios and you might have to go a shade darker across all of them to standardize the color but that is difficult to say without seeing the windows.

would using a toner help with this? I included a pic of one window. we called a professional & he said a toner would darken the pine to match but would like to know your thoughts. thanks.

"would using a toner help with this? "

Only if you cn find someone who REALLY knows how to even up the color.

The toner is NOT applied in a uniform coat.

After the color is fixed, a clear top coat is applied to protect everything.

The trim looks more blotchy than the windows.I think the variations in color is normal especially with a pine. The only thing that looks bad is the color match to the trim. Did the contractor provide a stain sample before the work was done? Usually when I bring in some wood to be matched my painter usually says what part of the sample do you want me to match.I never use conditioners either and don't like them. I would recomend to have the painter to do 1 window first this go around.

You just need to get a better painter. The following photo is of pine window interior and poplar trim. Poplar has big dark green splotches. I was really worried about the match. Good painter = good results.

Nice job on the Poplar.
It looks like the pine vs. trim situation was just a poor match. I'm sure you made it clear you were trying to match, didn't you? A sample or samples would have definitely helped.
A remedy will need the same thing; SAMPLES. I would recruit a painter willing to take the time & energy to get a good match, teaming up with the paint store to do so although some will mix it themselves. Be sure he uses parts from different places on the job as pine is characteristically uneven just by nature.
Was the first try top-coated with poly or something similar?