Sorry for the bump on this, I can't believe it has been over a year since the topic started.
To run down the original start of the thread and close this and hopefully, someone finds it helpful. Originally, I bought a new CTV cover because the casing cracked during a -10 degree cold start where the battery wouldn't work. Cranked it hard and I broke it.
The rattling ended up going on for another set of great time. Until about 1.5 months ago until I (after 4.5 years) decided to check clutch springs and was advised to replace entire clutch. On inspection, the starter pinion was busted and was the result of said noise.
That was replaced along with the clutch. Still starts fine, I don't have that rattle and now I am around 1,600 days of riding my Kymco A50. I am around 25k miles on it and we are set to test a fifth winter here in Indianapolis, IN. I need to clean the carb here soon, haven't done that since mentioned in this post and adjust the idle a bit higher to get ready for it.
Thanks peeps, sorry been so long since I visited. Got caught up in school and such.