I can confirm that, by default, a "make install" will not mess up your system. You can have a look at modified paths looking at the "configure.conf" file, you'll see that everything is done under /usr/local/ subdirs, making all this ... safe
About build scripts, here you are small tips :
comp.sh: static Raydium / dynamic external libs without ODE (not so useful, except for small things like most game servers, that don't requires ODE, so the binary is a bit smaller). Static Raydium compilation allows you to have multiple version of Raydium at the same time, making some tests easier, it also safer in some cases, since breaking Raydium will not break already compiled binaries. But it's slow like hell, and is not very suitable when using Raydium "as is".
ocomp.sh: same, with ODE.
odyncomp.sh: dynamic Raydium (libraydium.so) / dynamic external libs (jpeg, ogg, xml, …), with ODE. You should see this one as the default for most Raydium applications.
ostatcomp.sh: static Raydium / static external libs. This one may be very useful, for instance when releasing an application. It will create a huge binary (I mean, really huge !) with almost every single library statically linked. This binary will probably run on every Linux distribution and version (binary loader and OpenGL apart). It's very hard to use this script, because of the need of a lot of static ".a" libraries, that may require to install many packages from your distrib ... and even hand compile a few one. Not the usual way to compile with Raydium, you see
Long story short: use "odyncomp.sh" for most cases, but try "comp.sh" for you game servers.