When writing Javascript and CSS Templates it would be considered like writing separated .js or .css files, no <script> or <style> or <link> tags should be added in those templates. Those Tags are being added automatically by CJT Templates linker. Adding those tag would break those Templates.
Embedding Template is current will embedded Javascript and CSS templates without any tags appended. Its still a good practice to follow the Above strategy of avoiding adding any Tags as next CJT release would start adding those templates while embedding too.