Shopify Apps in general do not have access to see what the fees are for orders that are not Shopify Payments.
For PayPal there is an easy solution:
simply set up the PayPal bank feed in Xero
then you'll see the transaction and fee as two separate items
You can match our invoice to the transaction and code the fees easily
The other thing you'll see in that feed is the withdrawal (payout). You can simply reconcile that as a transfer to your bank account and you're done,