If there's a way to open the KDE/Qt file chooser dialog from the command line, it might not be too hard to modify Fl_Native_File_Chooser (FNFC) to invoke that, using its API to control presetting the browsing directory, choosing file|directory browser, etc.
Actually, providing a generic way to tell FNFC thru its API to invoke any command line tool to open a file browser might be useful, as apparently these tools change names almost as often as new linux distros are released (i.e. often).
I understand zenity(1) was the way to do this in GTK, but it's been surpassed (I think) by yad(1). KDE has something similar, e.g. kdilog --getopenfilename from what I can tell.
FNFC could invoke this command line tool in the background with fork() and pipes so as to not to block the FLTK app loop while the browser is open, and on completion, returns the user's chosen file through the API as per usual.
In this way the application can choose which browser is used, and perhaps even support different command line file choosers by probing to see what's available (e.g. looking for kdialog, yad, zenity, etc) without FLTK having to track all these different tool names.
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