I live in Qubes Whonix too, for the past couple of years.
I don’t experience this issue at all, on any security level. I have a different issue, not sure if it’s Whonix related or not but onionsites consistently redirect to HTTPS thus breaking the connection, and I often get connection errors instantaneously when loading something, which are solved by refreshing right away.
Most likely different issue from Clearnet websites partially loading issue not caused by Whonix.
The same issue should happen on Debian when using the Tor Browser Bundle (TBB).
Please try to resolve as per:
If the onionsite you are attempting to reach times out, Tor Browser may attempt to upgrade to HTTPS. In this case, the behavior is normal and can be resolved by changing the Tor circuit if the onionsite does not support HTTPS and changing the URL to use HTTP instead.