Good question! You can create a Credit Note, which will indeed shift the liability and will correctly reference and update the prior legal invoice. If you’re refunding a PaymentIntent however, we won’t shift the liability. Basically, we offer you two ways to move money back to your customer: one that might be a higher lift which ensures your accounting is updated and the liability if shifted, or a much easier way to refund, but you may pay some tax out of pocket.

“Higher lift” means “more work” in this context.

Presumably because it's hard to do correctly, and Stripe chose to focus on the easier part.

For example, I need to report VAT on the 15th of the second following month. If I got a refund after that date, I have already reported that tax, and I need to report a correction. I can't just report a lower tax the next time.

If you don't have a lot of refunds, then just paying taxes that you don't owe may be cheaper than handling it correctly (which is a lot of effort). And it may be the safer option -- nobody is going to fine you for paying too much tax.