Look, I'll be very honest, I've already configured 802.1x using Freeradius, NPS and ISE and I've never had any problems.
There is probably some configuration missing in FortiAuthenticator, but unfortunately I don't have expertise with this tool.
It would be interesting to open a support case with Fortinet.
I am not a Cisco Meraki employee. My suggestions are based on documentation of Meraki best practices and day-to-day experience.
Please, if this post was useful, leave your kudos and mark it as solved.