I seem to remember some talk about having a package like this, so I thought I'd try putting something together.
Essentially this uses mtree to generate the default filesystem layout under ${LOCALBASE} and then generates the corresponding pkg-plist. Recent changes to the ports infrastructure mean that when the last file in eg. /usr/local/bin is removed, that directory would be removed. Now, this should really not make a gread deal of difference in normal usage, but the fact that some well know directories may come and go arbitrarily seems to cause some alarm and despondency amongst developers and package building tools that have certain engrained expectations about the way ports works. There's also an argument that pkg(8) ignores any changes to ownership or modes of mtree files and will delete them willy-nilly, but that seems counter to the idea of what mtree(8) does in any case.