Yes, if you purchase the PDF Embedder Premium Secure version then you can switch between 'secure' and normal modes. You should not also purchase the regular PDF Embedder Premium version.
In Settings -> PDF Embedder / Secure tab, there is an option "Send PDF media uploads to 'securepdfs' folder". If this is checked, subsequent PDF uploads will be uploaded as 'secure', and embedded as such when selected for inclusion in a page. If unchecked, uploads will go to the normal media uploads area (outside the special 'securepdfs' folder), and will be embedded as normal without 'secure' protection.
You can find out more by reading the Secure Instructions.
It is also possible to ensure your 'normal' PDFs have a download button available to your viewer, but your 'secure' PDFs do not. To do this, set the main Download Button checkbox to on or off depending on whether the bulk of your PDFs are likely to be secure or normal - do this in the 'Main Settings' tab of Settings -> PDF Embedder.
Then for individual embedded PDFs you can add a 'download' attribute to the shortcode if you wish to override the global setting. This is described under shortcode parameters - you would insert download="on" or "off" before the end of the shortcode: [pdf-embedder url="..." download="on"].