I found that for some reason if a user checks out with a different currency like CAD, coinbase is much more likely to show the transaction as underpaid by something like 2 cents (even though it still shows it as completed/paid), and that results in a payment error on IPB and an admin having to manually add their purchase. Changing the default currency of my store to USD fixed this and now I only have to manually add transactions if the transaction was actually underpaid or overpaid.
Still hoping to see support for flexible payments in a future update.