There's no problem here. Just because ports use perl5.24 or perl5.26 for their own purposes has no bearing on what you use for your own personal projects. perl5.24 and perl5.26 install to different locations, do not conflict with one another, and can be simultaneously installed and used. Install and use whatever version of perl you want. Install whatever variant of the perl5 port you want, which is how /opt/local/bin/perl and related symlinks get set to a particular perl version.
If you have been using perl5.24 and p5.24 modules for your own projects and now want to use perl5.26, simply install the p5.26 versions of the modules you want. Ports that require a perl module must specify a dependency on a specific perl version of that module (e.g. p5.24-... or p5.26-...). Ports must not declare a dependency on the perl versionless "stub" port (p5-...). I have not used FreeBSD and am not familiar with the UPDATING file.
