I've been using after effects templates for many years now, using them to create engaging opening's for my wedding videography business. During these processes i've had to alter the scripts, making changes to backgrounds, screen text, and making minor adjustments to ensure the templates are fit for the finished result.
I currently use version 5.5 of the after effects application to complete my work.
After the template has produced the desired video, i would then use an editor such as premiere pro or final cut pro x to add any potential audio.
The resulting video file can then be converted back to any playback format as required.