Thank you for the detailed explanation. As you will have deduced, I have been using the second option, the build in the source tree.
I can switch to the first option so that the issue disappears for me. If Gnulib is not going to be extended to support the second option as well, it may be a good idea to add something along the lines of your remark above to section 3.12 of its manual ([1]).
If Gnulib is going to be extended to support the second option as well, I am not yet sure how. The problem is that the same source tree would have to support both options to support both kinds of developers. This rules out the "--vc-files" option because it would appear in "bootstrap.conf" (if "gnulib-tool" is not used directly), which isn't developer-specific.
If development model #2 is going to be supported, the only feasible option I see here would be to add the autogenerated header files non-conditionally (and to rely on user-provided ".gitignore" fragments to ignore object files, log files, etc.)