The CMS is running on our apache. This perl-based webserver they provide is only used for debugging and not more. I can assure this 100%.
It's hard to put all information in a question. I could post the apache configurations if that could help. Basically for this CMS you have to install a webserver (in our case apache) and mod_perl. That's it. In the configuration, setup sources where perl should look for Packages and you're ready o go. That's why I tried to simplify the question as much as possible.
Basically I just want to use NYTProf on a webserver and profile everything, even if it runs "inside" mode_perl.

Update: The CMS is called "Imperia". To run the CMS you have to extract the CMS itself and add

    PerlOptions +Parent
    PerlModule Apache2::RequestRec
    PerlModule Apache2::compat

    <Perl>
        unshift @INC, '/mycms/develop/site/modules/core';
        unshift @INC, '/mycms/develop/site/modules/collection';
        unshift @INC, '/mycms/develop/site/modules/fallback';
    </Perl>

    <Location ~ "/imp($|/)">
        SetHandler modperl
        PerlResponseHandler Imperia::Core::Backends::ModPerl20
    </Location>
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to your webserver configuration. To get NYTProf running I added

    PerlSetEnv NYTPROF file=/mycms/nyt/prof.out
    <Perl>
        use Devel::NYTProf::Apache;
    </Perl>
[download]

as well.

So I don't think the issue is related to the CMS. It's more like a general issue that I don't get subroutines and stuff profiled which is using mod_perl. That's why I tried to simplify the question.