Not very elegant but you can add as an email header:

email.Data.Headers.Add("X-Mailgun-Variables", "{ \"variable_name\" : \"value\" }");

Thank you belidzs.

I tried adding "X-Recipient-Variables" to the header last week but with batch sending Mailgun seems to need that variable in the body, not the header. I ended up going with a basic RestSharp submission and everything works as expected.

Was initially sad that I lost Razor templating but with a batch I'm only sending one "body" and having Mailgun insert the variables to customize each message anyway! So really there's no point in FluentEmail offering this parameter! I'm closing this "issue".