Noted, but I can't comment on anything related to SWIG or Python.

That's probably due to some "old code" leaking into the "Modern CMake" approach. I didn't have the time yet to rewrite everything and I'm aware that there's still something to do.

At a minimum, I'm pretty sure this should be assigned to a target LINK_OPTIONS property.  Or, perhaps even better, a target POSITION_INDEPENDENT_CODE property (rather than appended to a string list of library names).

Yep, that's correct, and very likely it should be added to PRIVATE CMake properties rather than PUBLIC, hence it would not affect your build at all (PRIVATE properties are not included in INTERFACE_* properties).

I don't know the long-term fix for this.

I'll check if I can fix this.

In the short term, I'm going to attempt something like

get_target_property(templist fltk:fltk INTERFACE_LINK_LIBRARIES)
list(REMOVE_ITEM templist "-no-pie")
set_target_properties(fltk:fltk PROPERTIES INTERFACE_LINK_LIBRARIES ${templist})

Or something like that.

Might work but it's only a workaround.