They made it a bit better but pretty much as you think.
If you build sites in Muse they are more of a cavas website and its not really designed to build websites that offer proper control by a busines as a manageble website.
The edit only effects that page however that may still have some carry over… a menu bar for example. If you must edit a muse site after it goes up (temp) then I suggest importing the site (or page) into dreamweaver as that gives you a testing area away from the actual website which doesn't bugger your muse template… it's not ideal but better than nothing.
You can edit your muse site with the "Edit" mode in BC. It does affect your Adobe Muse file but as soon as you open your site with Adobe Muse the changes will be transfered. (You have the option not to merge the changes also).
However, I wouldnt recommend to change the HTML or CSS within BC.