If I remember correctly, the initial reason why gnulib used the GPL template for some LGPL file was because CoreUtils didn't yet use gnulib-tool at the time. The CoreUtils maintainers didn't want to manually change the files every time they were imported from gnulib.
I suggest we revert that decision: all files that really are under the LGPL should be labeled as LGPL files in the headers. If some projects doesn't want the confusion stemming from having LGPL mentioned in headers, they can use gnulib-tool --gpl which would modify the headers from LGPL to GPL (which is legally fine). CoreUtils now uses gnulib-tool, I believe, and could thus use this --gpl parameter. /Simon