Yes, if you pay thru Paypal, there's the hassle that to track down where the money went, you have to take an extra step. If you buy something from, say, Foobar Company with a credit card, then the transaction will show up on your credit card statement as "Foobar Company". (Usually.) But if you pay with Paypal, it can show on your credit card statement as "Paypal", and then you have to go to your Paypal account and look at their transaction list to see where the money really went. And of course if you deposit money with Paypal and use that to pay bills, or if you use money that was paid to you with Paypal and that is sitting in your Paypal account, to pay bills, then there's no way for Paypal to connect a particular deposit or receipt to a particular payment. At that point you have to treat Paypal as a bank account and not simply as a flow-thru transaction facilitator.
If you use Paypal a lot, that's not a big deal. I briefly had a small business where most of my receipts came in to Paypal and then I paid bills from there, so I just treated it as a bank account and used information from their statements for my accounting and taxes and so on.