With the vast majority (99%+ of non-card Euro transactions, and a substantial majority of card Euro transactions too) going via SEPA in Europe these days, the benefit of Paypal is much reduced. It is competing much more with card payments these days than with direct transfers, given the combination of SEPA and even faster local schemes (e.g. in the UK, a huge proportion of smaller charges go via Faster Payments, which will sometimes be near instant and usually below two hours).
I still use Paypal quite a bit, but because it's simply convenient to use it and be able to change where my payments go from (which card/account etc.) without having to change what's on file with merchants.
If you would use SEPA for an SAAS registration, how would you handle the waiting time of multiple days? Accept the customer without prove of payment or ask him to come back in a few days?
For SaaS it's easy, you just treat the payment as a success. If it ends up failing, you treat it as a chargeback.
For selling goods that you hand over (e.g. irrevocable product keys) it's much trickier and depends on the specific business whether it makes sense to have the customer wait.
I still use Paypal quite a bit, but because it's simply convenient to use it and be able to change where my payments go from (which card/account etc.) without having to change what's on file with merchants.