Stripe → Balance → Payouts → Export. Payout-level is what actually hits the bank.
Same date range, CSV. Note that Stripe payout dates and bank posting dates differ by a day or two.
Each payout carries an ID that appears in the bank description. Match by it and collisions disappear.
Don't book per-charge fees; total them from the balance export and post a single monthly fee entry.
Only unmatched payouts matter. Refunds and disputes explain nearly all of them.