BC lacks word wrap for technical reasons. The Beyond Compare interface is giving you visual control over some powerful things. So far, Scooter has favored that power over the (seemingly simple) feature of wordwrap. Never say never, says Scooter (Version 5?) but the bottom line: wordwrap in Beyond Compare is not as simple to implement as it seems.
So for now, when lines are over 100 chars long, I:
1) go to over under layout:
view->display over under.
2) If that is not enough, I zoom out with the shortcut key: Ctl + Shift + Scrollwheel (exact key varies per Mac/Win/Linux).
3) Finally, I inspect really long lines in the bottom mailslot window.