It's probably not.
Onions connections are more sensitive than non-onion connections, specifically sensitive to the date and time being accurate.
It's not uncommon for people to have issues connecting to .onion websites, while non-onion websites work due to their time being out of sync so it not being an onion might cause less confusion for users.
The Tor Check is subject to false positives (it says you're using Tor but you're actually connecting directly from an IP that is also an Exit node while not using Tor) and false negatives (it says you're not using Tor because the Exit node hasn't been checked and added to the database of known Exit IP addresses yet). It is a best effort but won't provide 100% accurate results all the time.
(There's also the potential for a malicious DNS server to respond to a DNS query for a .onion domain with an IP and trick the user into believing they're making an onion connection when they're not but I think that's a little more far-fetched than the standard use case of "Make sure my Tor Browser is connected")