(this part is about a bug)
Forcing magic links for RFC, ISBN and PMID without simple way to disable it through configuration can't be seen as anything other than a bug.
it is clear that the changing the default behavior will create a serious regression, so the default behavior should be exactly as today. however, not allowing to disable these magic links through config is a bug. i might not want my wiki to link to either of these external sites.
(this part is about enhancement)
moving it to configuration, if done correctly, will also allow sites to expand to other magic words, such as bugzilla entries for the project this wiki is used for, or patent#, or court ruling etc.
each of these may be more relevant or more appropriate in some specific wiki than RFC or ISBN or PMID.
unfortunately i can't add a patch to this ticket (maybe i will, eventually, if nobody else will), but the idea is to use something like $wgAutoMagicLinks array that will receive a value in DefaultSettings.php that will create the current behavior, and the user will be able to override in LocalSettings.php, for both removing unwanted automagiclinks (some or all), and add new ones.
again, the ability to have new ones is "nice to have", but not being able to suppress the hardcoded ones through config is nothing less than a bug.