The ebuild does some work to rebuild all the autotools where configure.in is, but eautoreconf is already recursive by itself, so a single call *should* be enough; please check that and fix, right now it's wasting quite a bit of time in src_prepare.
Created attachment 212823 [details] Build log
A single call to eautoreconf is indeed enough, and I changed this in the newer version. However this is barely cosmetic. src_prepare spends exactly the same amount of time autoreconfing the sub directories. The configure.in and Makefile.am files would need too much dev time to be worth simplifying to do it in a single call. CLHEP used to be a collection of packages which merged into one. Upstream is now in a bug-fix mode only.