I'm not an expert at Apache, exactly, but I can tell that you need to be more specific about the changes you're making, and why, before anybody can help you find a way to avoid doing that.
As I understand it, Apache provides a module called suexec to allow cgi's to run as the user that owns the directory. Without suexec cgi's run as the httpd owner which is typically a 'nobody' user with highly restricted permissions. So to allow e.g. mypgm.cgi default permission to write to a file in /mnt/web/guide/guido (user Guido's root) with a chmod of 644 Apache must be recompiled with suexec enabled. I failed at my attempt to do this and didn't want to keep plugging away so have just chmod'd my (local intranet) root directories to 777. It's a lousy kluge but it does permit me to keep working.
A lot of workarounds tend to be just as much of a security concern as suexec is itself.
Not sure security's an issue on my intranet, but inevitably working improperly will lead to improper results and security issues on the production server.
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