Yes you are right!
This CSS zooming is a crude hack. I think it basically treats a web page like a pdf document where you just enlarges everything.
When you zoom manually, safari does a smarter sort of zoom where it enlarges but tries to keep widths of the elements the same size, reflowing text where needed and scrolling only when necessary.
If the web page has a fixed size that is smaller than your browser window, like this forum, css zoom works ok. But with a page like gmail, which has no width constraint, you get into trouble.
Hmm, wait, I just checked out wiki, which also uses up all available screen real estate, but does NOT have this problem.
Notice in gmail, even if you zoom way out below what should be 100%, the login is still off the screen. The font gets real small but the width of the page stays the same. The css zoom basically "sticks" and isn't completely reversible.
Bottom line: you have to decide which is more annoying: having to hit Ctrl+ for every tab you open, or running into some problematic pages.
On Windows, I use autohotkey (a kdb and mouse macro scripting program) to switch off the CSS on the fly when I need to. I think Mac has similar capability built in, right? If I were really clever, I guess I could program autohotkey to send a few ctrl+ whenever it detects a new window or tab in safari, but I'm not there yet.
Bottom bottom line: Apple needs to add this feature. It's a pretty basic accessibility feature. Doesn't Apple have like an accessibility guru/advocate?