About 1 - You're talking about extract zip file in OpenKM. In your case you want all files with same metadata, but you should understand it's not the normal caes, normally users apply different metadata to different files. The idea from version 6.0 is apply metadata to several files at same time (
http://www.openkm.com/en/openkm-massive-actions.html ) I think with it you can solve major problems ( now is only remaining make it recursive too, that's the only case we still have not yet implemented ). This solutions in two steps complains with your needs and general users. I will investigate if it's possible doing it on a more direct way, but it makes logic more complex, because now we ask for metadata after doc has yet uploaded ( one file ), if there're several, folders etc... will be more complex and that what seems stupid feature could be more complex than seems. I will thinking about it.
About 2- Icon greyout ? I do not understand what are you talking abou ?
About 3- Default installation with default metadata should run correctly ( any problem on administration registering ). Remember in version 5.1 after registering you can not delete or change some properties ( to maintaining historic consistence ). You should not change DTD only cnd and xml files. DTD is used to validate xml file you have no need to change it, if you change it's normal not run correctly, because OpenKM is prepared to working with this DTD and not other.