I love that you found a workaround, seems to be from this StackOverflow post (detailed information can be found there) but careful:
- the registry path you posted is not modifiable if you are working as non-admin user, which everybody should
- the consequences are unknown if you change the default engine for all .js files, and all the existing DOpus scripts, and there might be other programs (or in corporate environment admin scripts, etc) which depend on the old engine
But I love that DOpus accepted it without obstacles, although extensive testing is needed. As I posted here both jscript9.dll & chakra.dll are apparently COM objects, what DOpus also uses. It'll be much safer for all if DOpus changed its own engine only instead of this solution, or better yet give more adventurous people like us here the option to select the engine in prefs (v5.8 or v9?), and we'd gladly give feedback about compatibility, etc.
Feel free to bug devs like I do 
Squeaky wheel gets the oil (don't kill us Leo/Jon)