Upgrading ports with options

I know some ports use make config, some do not, etc. If one has build a port, say Apache, with custom make options, say to turn on suexec for example, I take it you cannot simply say portupgrade apache22 as then it will be upgrading all right, but, without your make options.

Other than tricks like storing them in make.conf, any other hints? Or, am I just wrong?

If ports use make config, and I set them, will those be respected when using portupgrade?
Options from 'make config' are stored under /var/db/ports/[portname]/options. They will be re-used by portupgrade (it will print something like 'Found configuration options from [version]'), unless the set of options changes. Portupgrade will then invoke 'make config' again.
As you said you are using portupgrade, you can have a look at /usr/local/etc/pkgtools.conf.sample and create your own pkgtools.conf.
Search for MAKE_ARGS and look at the examples.

It should be honored by both portupgrade and portinstall.