Hello sf, unfortunately, native theme details are not exposed to the add-on, or I didn't find how yet, although I searched for it ... If you find an add-on who is capable of reading the current theme and apply it, can you point it to me so that I can analyze how it does that ?

Now, I guess you're saying that somehow the theme you chose is imposing its value to the searchbox, preventing it from inheriting the body settings I made.
I tested the Dark theme under Windows and Linux, and nothing such as what you describe is happening = search box text is black as I specified.
=> would you be on IOS ? (I can't test it, I have none)

Probably better if you can open an issue so that I can track its details with you, if you agree -> https://github.com/aaFn/Bookmark-search-plus-2/issues

Note: in 2.0.57 I am forcing black on the search box, based on your feedback. I hope that will cure at least the visual problem and make it useable .. let me know. Thanks, aaFn.

*******************Edit**********************************
As of 2.0.68, the functions to read and adapt to FF active theme, or to set text and background colors at will, are now available, and used by BSP2 as options.