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When building Epiphany with gtk-doc or introspection support, Webkit's icondatabase directory and WebpageIcons.db is created outside build environment (in user's data directory: ~/.local/share/webkit)
On Gentoo, packages are built within sandbox environment - therefore when something is created outside the build environment, the build fails with access violation error and this error happens in two cases:
1) When building with introspection support, access violation happens when it runs the ./epiphany --introspect-dump=...
2) with gtk-doc, the violation happens during: "gtk-doc: Running scanner epiphany-scan" phase.
I have no idea how these scanners work, but the database creation code is inside the webkit_init() and it seems that webkit_init gets called in both cases, thus causing the access violation.
Ok, this really isn't this big of a bug, as apparently the icon database is written to $XDG_DATA_HOME/.local/ directory.
Closing the issue.