Thom, thanks for the clarification on +server, I'll update that point in the post.
You're absolutely right to point out the use of versions in executable names. I just ran into this while writing a shell script that calls mysqladmin. I didn't realize that I needed to call mysqladmin5 :)
I suppose sysadmins have differing opinions on configure/make/make install vs port systems— largely based on Unix skill level and server environment constraints.
I think that it's harder for those with lots of command line experience to get used to build locations other than /usr/local. I doubt that it's difficult for those who are relatively new to the command line, especially since they can see the contents of /opt/local in the Finder, which makes it easier to edit configuration files.
I'm starting to see some of MacPorts shortcomings with PHP extension selection. Someone recently asked how to install PHP's dBase extension, but didn't receive a timely response. Admittedly, dBase is not in high-demand, but it appears compiling PHP from source or using Fink might be the best way to add these extensions.