Each XSL-FO implementation (FOP, RenderX, AntennaHouse, Arbortext) is slightly different so you may find the XSL does not work perfectly or needs some updates to work in different environments. DITA-OT stylesheets are designed for Apache FOP so may not work perfectly outside of FOP.
Having said that, PE is extensible and readily allows integration of third party Java classes. Eg. you may be able to call DITA-OT itself from PE to render the FO documents.
Alternatively, PE itself ships with built-in DITA support which should produce PDF of acceptable quality. If you are going to use PE then that would be the easiest path to try first.