You can't modify apache's global configuration from within a request. People sometimes ask for this, but it can't be done with the way apache is structured. All that you can affect through the apache API is your own request, just like in FastCGI.
How would FastCGI prevent mucking with the perl interpreter? In both cases, the interpreter is persistent and perl will not prevent you from changing things that affect future code in the same interpreter.
Running as suexec would make a difference. The equivalent mod_perl setup would be to run a separate mod_perl backend for each user, which I've done in dev environments but it's annoying to set up. The security would then be identical, but it would use more memory than a shared server, just like suexec FastCGI would. In both cases the lack of sharing from copy-on-write is costly.
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