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application 4950 is part of 11.2 XE, not part of APEX 4.0, so you don't have it on any other database running APEX 4.0. (Well, unless someone used a hack to export this application from 11.2 XE and imported it there). If you install a standard APEX instead of the one that shipped with XE, you'll lose all XE-specific extensions. This has been the same with the management application provided with 10.2 XE - if you installed for instance APEX 4.0 as upgrade or fresh install on top of this release, you had "just" a standard APEX.
Of course you could ask why this application isn't migrated like user applications. As far as I know, no "system" application (area 4000+) is migrated. For the internal applications is obvious - they get updated and hence reinstalled. This XE management application is, as I said before, not part of APEX, so it is not maintained by the people who develop APEX. If they would just migrate it to a new APEX release, it's likely it would either not work or possibly mess up your system, as at least the APEX internal parts will probably have changed enough to make adjustments necessary. Of course you could claim you'd like the XE development team to support other APEX versions as well. But that's the point in XE: There is no support, no updates, whatsoever. The possibility to upgrade APEX at all is the big exception, but it somehow also proves the rule.
Thank you for your answer, I was afraid of that, I saw that when I have upgraded 10g XE to APEX 4. But I hoped that this time, on 11g XE, the things has been changed.
There is still a chance in the final version of 11g XE to have the latest APEX 4.1 included. Anyhow, this is not an issue as the APEX database application is not as useful as the administration web page of Oracle 11.2 database (full version), but it was nice to have it.