And update to this issue:
I also emailed itch-io support with this and received a reply from them stating
"We're not showing any purchases linked to this email"
The email I sent to support was the same address as on my account, so I'm at a loss a to why they wouldn't be able to find this, especially since they originally sent an email to the same address stating that my Meeple Station steam key on this account was ready (eg It proves in my mind that there systems are reporting correctly). I have sent them the invoice for the purchase from their systems as well as the paypal transaction id.
Just to recap: Itch.io are sending me e-mails to my address without issue (An automatic one stating I have a key, an email when I had to verify my account and another from their support team). However emails from their system which actually provides the key isn't and isn't in my spam folder. Their support teams current approach is by claiming that I've not paid $18 for the software.