I have noticed this myself, even in the admittedly simple uses I've put these two. One my sites is based around templates originally generated by PHP3. Given PHP's security problem with multi-part forms, I decided to implement an upload process using perl.

In doing so, I found that I had to re-design my template process to make them easier to share between PHP and perl. While a reasonably trivial task, it did take some time that I could have used for other portions of the project.

The lesson, then, is to take some extra time during your design phase to make sure that your implementation can suport multiple tools and processes.