Hello @acaparrelli,
The only thing you can do is trust the certificate. It is a Filezilla “feature” it doesn’t check the CAs that your OS trust so you need to manually trust it in the first connection. No matter whether it is a self-signed certificate, a let’s encrypt cert or a commercial one, in all of them, in the first connection, you need to trust it.
Edit: For more info you can check this post in filezilla forum.
Cheers,
sahsanu