I ended up with a reasonable option (commit 28cbc58): in stage 5 (‘%boot5-inputs’), most of the base packages get rebuilt against the new libc, so they can load the new locale data, but they are rebuilt using the bootstrap Guile.
In that stage, we also create wrappers for ‘%bootstrap-coreutils&co’ (Coreutils, tar, gzip, xz, etc.), which unset ‘LOCPATH’. This is faster than rebuilding them and it’s sufficient since these programs typically don’t run sub-processes (if they did, then those processed would have an unset ‘LOCPATH’, which would lead to inconsistencies.) Comments welcome! Ludo’.