At the moment there is no way to do eBay customer support on Freshdesk. eBay is blocking Freshdesk messages. eBay has been setup to accept sending messages from our support inbox and Freshdesk was setup properly to use same inbox. Here is an example of eBay message:
Oops. We weren't able to send your message to XYZ, because the email address you used to send this message, firstname.lastname@example.org, isn't linked to your eBay account.
Somehow eBay doesn't see that Freshdesk is sending messages using 'email@example.com' address
eBay masks the email address of every user and provides a custom generated address to which you can respond from your eBay vendor portal. So, the emails sent from Freshdesk gets blocked at eBay since it is not validated to send messages to the user.
This can be solved by integrating your eBay account as an e-commerce channel in Freshdesk. This is available from the Estate plan onwards and you can find more details about the integration here.