Ebuild has comment: # Note: xpyb is used as the C header, not Python modules so what x11-libs/xpyb is doing in RDEPEND?
good question. However, it doesn't make for a broken ebuild. While it's needed in DEPEND, it does no harm set in RDEPEND. Can you do a runtime. Nikoli read the doc/reference/surfaces.rst and it appears to me that it is indeed utilised at runtime. See .. class:: XCBSurface. That indeed appears to give the answer. In order to make a case that it not be included in RDEPEND you need to prove it's never utilised at runtime.
Fixed in 1.13.1 in the tree.