The root partition is essentially where the system binaries/configs go. In the bad old days every piece of software used to get dumped out to /usr or /usr/local. Sysadmins being who they are hated this because it meant that a bunch of crap was installed into the root partition that wasnt part of the base OS or required for the base OS. This is a pain in the *** for several reasons.

1) Restoring the OS became a royal hassle
2) Backing up the root partition became a royal hassle.

So the /opt partition was born and all third party software was meant to be installed to it. Good in theory, not so great in practice - a lot of the old legacy code etc still wanted to install on /usr. Optifying - which you may have heard of - is the process of changing where the software is installed to the /opt partition. Its not a large task but its one devs usually leave until last when porting software.
Now we get to the part about repositories. extras-devel and extras-testing come with these warnings every time you install a piece of software which basically says "Hey this could ruin your N900". The choice of listening to that warning is yours. If you choose not to and brick your device that leads devs etc to point and laugh - Nelson from the Simpsons style. Its not Nokias fault - nor theirs. The testing and dev repositories are for ..... testers and developers - people who as a rule know what they are doing.
You should never just shotgun a bunch of software onto your N900. The best rule of thumb is - install one piece, use your machine for a while and make sure its not broken (I suggest at least a day). Then and only then install another. This of course applies even to the extras repository as well, but to a lesser degree as software there should be at least optified.