Saving this to explain why software is hard.

For a long time, inode numbers from readdir() had certain semantics. Supporting overlay filesystems required changing those semantics. Piles of software were written against the old semantics; and even some of the most common have not been upgraded.

FWIW, if you are cross-compiling, while you might get a vaguely usable result by ignoring all of the warnings and letting worst-common-denominator defaults get applied, you absolutely should be paying more attention and either manually providing autoconf the answers it needs or (if at all possible, as this is more general) make sure to tell it how to run a binary on the target system (maybe in an emulator or over ssh)... you shouldn't just be YOLOing a cross-compile like this and expecting it to work (not to say that this wasn't a good bug in the fallback to fix, just that the premise is awkward).