Cannot speak officially for Moodle.org nor the folks that influence security decisions concerning the software restriction ... you are indeed correct, it is a software restriction.
You sound like you know what you are doing but sometimes ... other thoughts/ideas might spark a solution not yet contemplated or discussed.
While it's true that other packages run just fine, it means they use 'relative addressing' when linking to anything internal to the app and thus one can use 'transversal' links ../../../ (IF apache configured to allow - which most are by default and which I've had to do with an AllVideos Plugin to Joomla). And therein lies the issue (possibly). If the AV Plugin (example given) can be remote manipulated to transverse to other areas NOT under apache root then there is a security hole ... not in Joomla, but in the plugin. Joomla, however, does have a configuration item like that of Moodle and if set, the relative addressing is no longer possible ... can't go ../../../passwords or other location outside of Apache document root.
All that to say, Moodle takes that stance as default and makes it difficult to circumvent - period. While config.php hacks are the approach taken, there could be other files that also need hacking to make that work ... something one should be discouraged from doing ... cause Moodle will need to be upgraded - sooner or later.
In Moodle, anything created uses the wwwroot variable in the URL. So let's say you do use the workaround in config.php. Circuit A is down but you've a fall back/whatever configured to reach the same server on Circuit B ... the ONLY way all those internal links in Moodle can work is by using the SAME FQDN.
Ok, we know have a geographic picture of your situation now and can say that it sounds similar to geographic areas in West and South Texas.
Sorry, but I have to ask one more 'stupid question' ... this is all about accessing when students are away from school. So how much 'territory' does you school cover? And is that territory covered by one ISP for home connections? Is it typically that the circuit to the school (where Moodle server is located) goes down, but the same IP's upstsream and thus connectivity for home users/other customers is still up?
Maybe colocating your Moodle server one hop upstream from the school on the schools provider POP could be arranged.
'spirit of 'thinkering', Ken