It’s definitely tedious to track everything. I do like the import feature and it covers maybe 80% of day to day transactions but yeah it’s a pain to go and fix stuff. What your talking about with PayPal is what YNAB considers a transfer and payment and is usually part the 20% I have to fix. Bank to PayPal is a transfer transaction, PayPal to purchase is the payment. It can definitely get needlessly complicated and it sometimes automatically imports correctly, especially reoccurring payments or if the transfer is between two linked accounts.
Yes, paid time off requests or advanced request to use leave (doctor appointment, or other) is typical for any planned absenced in the US.