I would say that having your store on your home page is best, because most people will be visiting your site to buy beats right? Or at least browse them. So you might as well give them what they want straight away. And it saves losing customers who can't be bothered to look for the store
Having said that, the best thing you can do is test both ways, as not everything works the same way for everyone. If you haven't already, you should integrate Google Analytics and run your website for 3 - 4 weeks with your store on your home page, then 3- 4 weeks with it on another page. Then you can directly compare the results and see what works best for you
Regarding the chargebacks - there's no real 'Protection', but we do provide download tracking in Dashboard > Sales. Just click the blue order number and the ip address, date & time of the download will be displayed, and you can send a screenshot of this to Paypal/Stripe
It's always good to have a sale running. Some people run sales all year round, whilst others save them for special occasions. As you will be new to the beat selling world, it can't hurt to start with a sale to get a few more customers in
Some people put royalties into their contracts, but if you do, you are relying on the artists honesty to pay you, or you have to keep on eye on each of your sales to make sure you get what your owed, which is no easy task. So you can put it in but I would imagine the likelihood of actually receiving the royalties is quite low
Hope this helps!