The difference will diminish slightly as the waterlox cures; it's most profound when just applied, because the solvent has penetrated deeper into the wood. Look again after 24-48 hours.
You may be able to tone the lighter parts to better match the darker areas; that is a real specialty of pro finishers. It's an acquired skill.
There are so many variables that I couldn't begin to tell you what shades of stain to try. A pigment-rich gel stain may be the best way forward, but it could be that tinting the waterlox for the last two coats may be necessary. It's much harder to work with tinted waterlox than plain. The application becomes 100% crucial to avoid streaks.
Hopefully the disparity vanishes as it cures.
Casey

Thanks so much Casey.

I'm afraid it's already been a few days so WYSIWYG. We are already considering remaking/replacing certain pieces where the contrast is worst. And maybe a bit of gel stain here and there. Hoping that the additional coats of Waterlox, especially the satin top coats, will help.

Thanks so much Casey.

I'm afraid it's already been a few days so WYSIWYG. We are already considering remaking/replacing certain pieces where the contrast is worst. And maybe a bit of gel stain here and there. Hoping that the additional coats of Waterlox, especially the satin top coats, will help.