You're right about the change you already did, I think it's harmless. But, say, moving any installation location around would break all rpm build scripts as they require you to give exact paths to stuff. Not really fatal, but annoying.
Exclusivity? Is that the dedicated server vs. client/server hybrid thing? The previous ebuild handled that via use flags, which I'd consider wrong

Separate ebuilds for client and server are better.
The KDE icons and applnks are working where they are, if you or gentoo don't like that, either move them or disable them with --disable-desktop, then install them the gentoo way. The autopackage build does this, for example, because autopackage has way more sophisticated tools available.
The reason the rcd_scripts are not installed is that you're building a client only, there is no server to start, hence no scripts to be installed. What gets installed where is controlled from batch/Makefile.am via automake variables.
We don't change /usr/bin to /usr/games/bin because the latter is not in the path on many distributions. /usr/local/games/bin, which would be the bin directory for the default prefix, isn't even in the path on gentoo. What we really should be doing is, of course, to check what IS in the path and only deviate from our consistent scheme if we have to. Something to note for the future. And adapt the relocation code to it, it may get confused. For that matter, it may get confused if you set --bindir to something odd, because it needs to find from the executable path to the data path.
Data vs. docs: documentation isn't read by the program, so IHMO, it's not program data. I'm flexible about this for the furure as I don't really mind, but for 0.2.8.0, the docs should stay where they are.
The "Script directory not found" error is odd, especially the directory it's looking in. It shouldn't have more than one /usr/ part in it. The double /game/ part comes from you explicitly asking for it, it seems

Can I get your complete configure line again, and maybe all the output you can gather?
ICYDNK: set ARMAGETRONAD_FAKERELEASE=true before configuring, and your build will be way faster. Ideal for testing system integration.