Thunderbird somehow after torbirdy removed because of its outdated and not compatible with the current Thunderbird version, trying to link your email smtp/pop over tor hidden services just doesnt work. I tried this with riseup and danwin1210 email providers both doesnt work, Testing it using plain debian + tor + proxychains + thunderbird it will work fine.
I opened ticket with riseup they confirmed to me that all their servers working and they are using onion hidden services.
So the issue within whonix firewall or so.