A difficult question to answer decisively.
The tl;dr is that if you are performing highly sensitive activies you should not be doing them on the same device as your normal day to day activies. This is a concept called Compartmentalization.
To pull the answer straight from my own documentation on the subject:
When you take your whole operating system and stick it behind transparent proxying, everything goes over Tor if it can. Everything that goes over Tor will, by default, use the same circuit. Your operating system updates, your email, your browsing, and fetching information about media you play will all share the same circuit. The exit node could connect all of these things together and ascribe them to a single entity. This means things intended to be anonymous could be linked to things directly linked to your identity, or between psuedonyms.
See also: the Whonix Stream Isolation Infographic.
Another problem is that a lot of software is trash, it doesn't handle updates or fetching of content and files in any sane way. Again, from my own writing:
Some applications, even some security applications still check for and download unsigned updates over plaintext. This is not safe in any scenario but becomes a more obvious problem on Tor.
Now, these applications aren't bad because of Tor. These applications are totally unfit for purpose on the internet at all (ISPs get hacked, routers get rooted, wifi gets cracked, etc) but it is far simpler for an attacker to gain a Man-in-the-Middle position through being an exit relay in a Tor circuit (or posing as a free VPN provider).
So generally, no. You don't want to just Tor everything.
The alternative (where everything is torified, isolated and audited to be free of leaks) is very difficult to setup and you should also consider lateral leaks of information (an application that you don't torify might leak information outside of Tor about applications you are torifying because they're running under the same operating system and can infer information from each other). So do you consider your local ISP or a potentially malicious exit relay operator a bigger threat? This depends on your situation, there is no definitive answer but Transparent Proxying everything will always be sub-optimal.
