@meii sending this in the original thread since there's a 1000 character "chat" limit.
(tl;dr: To others reading, this is maybe a workaround to fixing the issue I reported. Instead of messing with custom FreeRADIUS or pfSense settings, I just made sure there is only ONE copy of the user certificate installed in the Computer Account and NOT any local user accounts (Standard Users, Local Admin users, etc.). And Same with the root CA certificate: only installed in the Computer Account certificate store, and this is accessed by going to "mmc" and then adding the Certificates snap-in then selecting Computer Account)
First thing I changed was made sure I installed certificates in only one trust store. So my current setup I have one "standard user" account that is my main account on Windows. And I have a "Admin" account that I only use for UAC prompts, etc. I think each one has its own certificate trust store. I.e. if you are logged in as regular/standard user, just do "certmgr.msc" and I made sure to delete the cert from Personal->Certificates and the pfSense root CA cert from Trusted Root Certification Authorities->Certificates. For the admin account, either log in locally or just do "certmgr.msc" again and right-click and "Run as administrator" and it makes another window. Even there, I made sure both the user certificate and the root CA certs were deleted. So now we want to access the actual computer's certificate trust store. I went to "mmc" and "Run as administrator" then File->Add/remove snap-in. Then add "Certificates" to the menu on the right and hit ok. Then make sure to select "Computer account" and Finish. I think (if I remember correctly) this is where I installed the user certificate for WiFi in Personal --> Certificates and the root CA in Trusted Root Certification Authorities --> Certificates.
I think doing all this makes sure there's no duplicate certificates. When there's two, Windows will pause and pop-up the drop-down thingy asking you to choose a cert before connecting, whereas with just one user cert (installed in the Computer account) it only has one choice.
Second thing I did was in the WiFi network settings (using WPA2-Enterprise still, EAP-TLS)... one way I got there was Control Panel --> Network and Sharing Center --> click on the network if you're already connected. I think if you're not connected it only lets you change settings when you start from scratch...not sure. Anyway we want the old Windows 7 or so window, not the newer one. So "Wireless Properties" where it has the two tabs at the top: Connection and Security. On Security tab, where it says "Choose a network authentication method" I made sure it was Microsoft: Smart Card or other certificate. I have "Remember my credentials for this connection each time I'm logged in" checked. Click on Settings. When connecting, "Use a certificate on this computer" and "Use simple certificate selection (Recommended)" checked. Didn't bother with Advanced button. Below it I have "Verity the server's identity by validating the certificate" checked and also the one below it "Connect to these servers..." and I put in the FQDN for the server cert in pfSense I'm using for FreeRADIUS (in my case radius.home.internal). In the list of Trusted Root Certificate Authorities below, I made sure only my pfSense root CA was selected and nothing else. At the bottom I have "Don't prompt user to authorize new servers or trusted certification authorities" checked. Lot of these prevent WPA2-Enterprise Wi-Fi attacks in the wild. So I think the relevant part for what you're running into was in "Advanced Settings" from the main "Security" tab. "Specify authentication mode" is checked and I put "User or computer authentication". Down below, I do not have that part checked where it says "Enable single sign on for this network". On the 802.11 settings tab and "Fast roaming," I have "Enable Pairwise Master Key (PWK) caching" checked.
So I don't know if any of the above settings in Step 2 helped except maybe the "User or computer authentication," but I definitely think Step 1 above helped -- making sure I only installed the user Wi-Fi cert and the pfSense Root CA cert in the computer certificate store via mmc Certificates snap-in. And made sure to first delete those certs from the Standard and Admin user accounts. (Oh! Note: I made sure to delete all those WiFi certs first to start with a clean slate because once you install them to the computer certificate store, they also magically appear in the "certmgr.msc" for both Standard and Admin user accounts, so it gets confusing.
Either way, Windows no longer prompts me to select a cert when WiFi connects, and I don't see the stupid "host/" prepend string or whatever in the pfSense logs. I haven't really tested if it logs into WiFi when you first boot up the laptop before logging in -- I think it did it! So in the end I didn't even need to learn all the weird FreeRADIUS syntax since it looked like a giant pain getting custom config settings to work with the pfSense FreeRADIUS GUI. Yuck.
I hope all this helps! Uh if you need screenshots lemme know since it might be clearer than a bunch of words. Hope any of this helps!