Counts toward inbox count.
Don't think this happened with HoT.
ArenaNet mail (doesn't count toward inbox): https://i.imgur.com/uyBXG8i.png
PoF Gem Purchase mail (counts toward inbox): https://i.imgur.com/0VVHI1Y.png
All my alts are just storage for my Engi.
This may just be intended and not a bug IMO.
"Sticks and stones may break your bones but words will never be able to injure you!"
The Grim Adventures of Billy & Mandy
It still has the ArenaNet symbol on it though, so I wouldn't really call that "regular" mail, personally.
The mail about the gems didn't have the gems attached to it; it was just a mail letting you know that the gems had been applied to your account. So, it's different from the Anet mails with attachments. Regardless, both mails have the Anet symbol, so it's all good.
Oh look. I have a signature now.