If you want ebook-viewer-portable.exe as well, in the PortableApps.com version, perhaps you should ask the PortableApps.com calibre maintainer?
I'm sure Kovid could put it in his portable edition (if he feels it is worth it), but it still won't show up in PortableApps. The only thing the PortableApps version uses is the binaries folder shared between both portables and the main install -- the portable launcher infrastructure is unique.