Back when Debian had Apache 1 as the default, it offered a separate apache-perl package that had mod_perl statically compiled. You could install the apache and apache-perl packages together side by side. Very nice.
Nowadays, with Apache 2, mod_perl is only a DSO, AFAICT, and I needed to set up my own parallel set of dirs, as I mentioned earlier, but it worked fine.
Since I'm not compiling my own mod_perl2, switching the Apache 2 version isn't an issue, since the packages all get upgraded together.