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I could be wrong here but as AWS manage the VPN across 2 AZ's which you cant configure or ever find out, I've a feeling they will not charge you for the Cross AZ because its a managed service.
Dont quote me but thats my theory..
This repost by Tushar_J explains it a little https://repost.aws/questions/QUVfEIk2sHT22u4Oww88aNKg/how-to-find-availability-zone-of-site-to-site-vpn-outside-ip-address
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I agree that this would be in line with AWS's general pricing philosophy: if you can't control (or in the case of site-to-site VPN, even know) whether you're crossing an AZ boundary, you won't be charged for cross-AZ traffic.