Dec 16 2015
I guess it does the job. However it makes the task of extension developers more error-prone. For the very least, it should be documented clearly (here?).
@saper: the problem with autoloading are use cases where the code of many extensions/skins should be deployed, but only part of them should actually be used. See the "wikifarm" use case here and here. If extensions/skins do not autoload (as in calling wfLoadExtension themselves), then one can choose in his/her LocalSettings.php, which ones one wants (using require_once or wfLoadExtension as appropriate for the extension in question).
Nov 5 2015
Thanks for the explanation! Is this documented somewhere? Since the mechanism is already used in REL1_25, which is out, it would be good to have documentation for it...
How does the plugin know which composer.jsons to take into account? Does the admin have to populate the include property in his composer.json manually or will the composer.local.json be generated somehow?
I am with @JanZerebecki and @bd808: To me it looks like disabling some extensions selectively is attacking the problem at the wrong end. I think that an extension should not be loaded (in the sense of wfLoadExtension) when it is installed with composer. In particular, this means that composer.json should not autoload the file ExtensionName.php. Rather should composer only be used to merely install the files, then the extension would be activated in LocalSettings.php using wfLoadExtension('ExtensionName') or require_once "$IP/extensions/ExtensionName/ExtensionName.php".
I just thought of an argument why using composer and another dependency manager at the same time might be a bad idea, at least if they are agnostic to each other.