There are some differences.
For one, the original battery causes the charger to terminate charge completely and the green LED on the charger will go out when its finished (on a 4A charger anyway). I really didn't like the fact that it didn't do this on the third party one hence I tested it. The last thing I wanted was to say leave it plugged in overnight and it keep pumping 4 amps into the battery!
As it turns out, I don't think it does this, so all is good, however whatever the mechanism is to switch off the charger, that doesn't work properly.
I use this to monitor the charge:
https://www.amazon.co.uk/Brennenstuhl-Eco-Line-Extension-Energy-Saving-White/dp/B01GLHLOG4/ref=sr_1_5?s=electronics&ie=UTF8&qid=1525798187&sr=1-5&keywords=Brennenstuhl+Eco-Line+Extension+Lead+Cable+Energy
Handy as I need an extension lead most of the time anyway
Also, I have a feeling the 3rd party battery charges ever so slightly higher voltage wise, than the stock Yamaha one (or perhaps its a case of Yamaha slightly under volt their cells to give longer life). because the bike will register 100% for quite some time before it starts to drop under this figure when in use. So maybe the true 'full' figure is perhaps 105-110% compared to the normal battery. If yours is showing 90 something after coming off charge, id be thinking that it may very well NOT be fully charged.