I've worked for FreshBooks and three other invoicing or payment related companies, and I have lots of friends that work at Shopify or run online stores.

Billing through PayPal is playing with fire. They can and do freeze accounts and it can take months to get the issue resolved. It will probably be fine, of course, but I've seen it happen and personally, if I were in a high margin business, I'd stick to Stripe. Especially if you run a company where other people make money on your platform like an Etsy or similar.